Re: [aroma.affymetrix] Error with process function: package sfit not found

Hi. The 'sfit' package is special, preventing me from submitting it to CRAN without a major rewrite. Because of this, it's not available from CRAN and there's no pre-built Windows binary for it either, which is what you're running into here. I basically have to manually build Windows binaries

Re: [aroma.affymetrix] Re: CalMaTe model fitting error

Hi. This is a hard-to-troubleshoot problem. This could be due to one or more arrays having weak/noisy signals, or possibly even being corrupt. As a first small step, I've created feature request https://github.com/HenrikBengtsson/calmate/issues/7. When that is in place, one can narrow down the

Re: [aroma.affymetrix] Error using RMA

Hi, so that example code uses the affy package of Bioconductor and not the aroma.affymetrix framework. It might be that there is a bug in the affy package or that it does not support custom CDFs well enough. It could also be that the chip type you're using is special and not well suited from

Re: [aroma.affymetrix] Error writing to connection

Hi. From your verbose output, I think two things can have happened: 1. This error happens when it tries to write to the file cache, which is located under ~/.Rcache/. It could be that this cache is using up your home drive/folder/account. Not sure what OS you're on, but to find where `~` is

Re: [aroma.affymetrix] Error: object 'csC' not found.

ame problem? On Friday, November 24, 2017 at 12:18:31 PM UTC-8, 321bi...@gmail.com wrote: > > hello , i called the csC <- process(acc, verbose=verbose) and them > print(csC), it still met Error: object 'csC' not found. > 在 2017年11月24日星期五 UTC+8上午7:41:23，Henrik Bengtsson写道： >> &

Re: [aroma.affymetrix] Error: object 'csC' not found.

Still the same; you're not calling csC <- process(acc, verbose=verbose) -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received

Re: [aroma.affymetrix] CbsModel or writeRegions error

I've been trying to figure where the error could show up and I have some "poor" guesses. In order to figure it out better, please install the developer's version of R.utils, which I just updated: source('http://callr.org/install#HenrikBengtsson/R.utils@develop') If the error occurs anywhere

Re: [aroma.affymetrix] CbsModel or writeRegions error

Hmm... assuming you're on a *nix-like system, see if there are any empty (zero-size) RDS files is: ls -la cbsData/gdsc_all,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY,paired/GenomeWideSNP_6/*.rds The original error message suggests that there could exist such a file. Also, you wrote "it systematically

Re: [aroma.affymetrix] CbsModel or writeRegions error

Hi, does the error occur when you run: fit(cbs, verbose=verbose) or did that complete successfully and you get the error while running: pathname <- writeRegions(cbs, verbose=verbose) If you run interactively, what does traceback() output if called immediately after the error occurs?

Re: [aroma.affymetrix] CBS input dataframe

Ah, my bad - you're correct. On Tue, Jun 20, 2017 at 4:40 PM, Emanuel Gonçalves wrote: > I think what I'm looking for is: > >> extractRawCopyNumbers(cbsmodel, array=1, chromosome=2) > > > Problem is I have ~200 and the function seems to be taking quite sometime to >

Re: [aroma.affymetrix] CBS input dataframe

Hi. There's no direct way of doing this, but as a start you can read in all the writeRegions()-exported segment data for all samples in a data set as explained in http://www.aroma-project.org/vignettes/NonPairedCBS/. That will give you a data.frame. >From there you should be able to manipulate

[aroma.affymetrix] aroma.affymetrix 3.1.0 release

aroma.affymetrix 3.1.0 and friends have been updated and are being rolled out on CRAN. These days I mostly do maintenance, fix bugs, refactor code, and optimize the performance of these packages. As usual, all released undergo rigorous validation based on system tests running for ~50 CPU hours

Re: [aroma.affymetrix] troubles in doing PCR fragment length normalization AROMA3.0

; exit(verbose) >verbose && enter(verbose, "Creating CEL file for results, if missing") >isFile <- isFile(pathname) >pathnameT <- pushTemporaryFile(pathname, isFile = isFile, >verbose = verbose) >ceN <- createFr

Re: [aroma.affymetrix] Error while setting up AffymetrixCelSet

Hmm... this looks weird but as usual, there's probably a simple explanation to it. Yes, it could possibly be that the CDF is incompatible with the CEL files, but in that case I'd expect an informative error message explaining why. In a fresh R session, what does the following output?

Re: [aroma.affymetrix] troubles in doing PCR fragment length normalization AROMA3.0

That looks like a hiccup in the file system or something. Did you try again? Also, if the error remains, please report what traceback() outputs (as the first command after you get the error). /Henrik On Wed, Jul 13, 2016 at 4:19 AM, wrote: > Hello, > > I

Re: [aroma.affymetrix] CytoScanHD_Array: problems with CbsModel(), 'Failed to locate Class object for class 'FutureError'

preprocessing (although I don't see how that should happen because everything is written atomically). If other tumor vs pooled normals work, then it is most likely a problem with the tumor sample and not the pooled normals. Hope this helps Henrik > > On Saturday, July 2, 2016 at 4:46

Re: [aroma.affymetrix] CytoScanHD_Array: problems with CbsModel(), 'Failed to locate Class object for class 'FutureError'

Also, install the following version of the future package: source("http://callr.org/install#HenrikBengtsson/future@FutureErrorFix;) This should reveal the true underlying error message. /Henrik On Friday, July 1, 2016 at 11:09:36 AM UTC-7, Henrik Bengtsson wrote: > > Unfortunate

Re: [aroma.affymetrix] CytoScanHD_Array: problems with CbsModel(), 'Failed to locate Class object for class 'FutureError'

_name, envir = assign.env) > > value > > }), new.env()) > > 9: eval(expr, envir, enclos) > > 8: eval(expr, p) > > 7: eval.parent(substitute(eval(quote(expr), envir))) > > 6: local({ > >value <- value(future) > >rm(list

Re: [aroma.affymetrix] CytoScanHD_Array: problems with CbsModel(), 'Failed to locate Class object for class 'FutureError'

Quick comment: Make sure all your packages are up-to-date and retry. If that doesn't work, please post your sessionInfo() after you get the error. /Henrik On Wed, Jun 29, 2016 at 1:32 AM, roman.hillje via aroma.affymetrix wrote: > Hi, > > I'm currently trying

Re: [aroma.affymetrix] "Error: Failed to retrieve genome information" + paired samples

Hi, comments below. On Fri, May 13, 2016 at 10:24 AM, Gaius Augustus wrote: > Hello, > I'm working on the Paired PSCBS protocol, and am running across an error. > > Here is my file structure > > -annotationData > ---chipTypes > -GenomeWideSNP_6 >

Re: [aroma.affymetrix] Incorporating Tumor Purity for ASCRMA / PSCBS

In the PSCBS package, we provide the `estimateKappa()` function for estimating kappa, which we refer to as "background signal", cf. https://cran.r-project.org/web/packages/PSCBS/vignettes/PairedPSCBS.pdf. The kappa parameter is strongly correlated with the amount of normal contamination. We're

Re: [aroma.affymetrix] doCRMAv2, Error: The fit function for requested AvgPlm flavor failed: median

gt; >> The solution is to update to a recent version of R, i.e. R 3.2.4. >> FYI, R 3.3.0 is coming in a few weeks. >> >> /Henrik >> >> On Thu, Mar 24, 2016 at 2:12 PM, Henrik Bengtsson >> <henrik.b...@gmail.com> wrote: >> > On Thu, Mar 24, 2016 a

Re: [aroma.affymetrix] doCRMAv2, Error: The fit function for requested AvgPlm flavor failed: median

is coming in a few weeks. /Henrik On Thu, Mar 24, 2016 at 2:12 PM, Henrik Bengtsson <henrik.bengts...@gmail.com> wrote: > On Thu, Mar 24, 2016 at 1:54 PM, C.C. <chenchen...@gmail.com> wrote: >> Hi Henrik, >> >> Thanks for you email. Here is the problem I enc

Re: [aroma.affymetrix] doCRMAv2, Error: The fit function for requested AvgPlm flavor failed: median

86_64-redhat-linux-gnu (64-bit) >> >> >> locale: >> >> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C >> LC_TIME=en_US.iso885915LC_COLLATE=en_US.iso885915 >> LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915 >> LC_PAPER=en_US.iso885915 &g

Re: [aroma.affymetrix] doCRMAv2, Error: The fit function for requested AvgPlm flavor failed: median

Hi, in order for us to help you, could you please: "[...] make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example." Thanks, Henrik On Thu, Mar 24, 2016 at 9:59 AM, C.C.

Re: [aroma.affymetrix] Re: CbsModel parameters

et 2 probes from one end and >> 3 from the other to be significantly different the middle you will get a >> significant result and a segmentation. I need to change the code in order >> to eliminate this possibility. >> >> Venkat >> >> >> On Wed, Oc

Re: [aroma.affymetrix] Error: object 'csC' not found.

On Sun, Jan 10, 2016 at 11:36 PM, <wxp...@gmail.com> wrote: > > Hi dear professor Henrik Bengtsson, > > When I was declaring the raw data set of CytoScan HD Array with > aroma.affymetrix, I'm encountering the following errors: > > "Error: object 'csC' not found

[aroma.affymetrix] aroma.affymetrix 3.0.0 release (10 years today!) - now with parallel processing

The Aroma Project turns 10 years today. Technically it's probably a few weeks older, but it was on Jan 11, 2006 that a few R scripts was put together to create the aroma.affymetrix. To celebrate, aroma.affymetrix 3.0.0 has been released and it brings some exiting updates including parallel

Re: [aroma.affymetrix] Re: Affymetrix Oncoscan library files

Ok, so that complicates how one would look at the pre-processing and how to normalize the signals, e.g. one should probably normalize probe signals of the two CEL files separately and only merge them after this step. A small first step would be to see if you can create a spatial image of the CEL

[aroma.affymetrix] aroma.affymetrix v2.14.0 released

Hi, aroma.affymetrix v2.14.0 (and friends) has been released and is now available on CRAN for all the major operating systems. Install/update by: source("http://callr.org/install#aroma.affymetrix;) This will take care of all dependencies and recommended packages as well (also those hosted on

Re: [aroma.affymetrix] How to: Create a CDF file from Bioconductor Platform Design (PD) Info package is miserably failing

Hi, thank you. I can reproduce this. Explanation and fix below. On Fri, Aug 14, 2015 at 5:27 PM, Guillaume Devailly gdevai...@gmail.com wrote: Hi, I was trying to run this : http://www.aroma-project.org/howtos/createCdfFromBioconductorPlatformDesignInfo/ to create a mighty cdf file for

Re: [aroma.affymetrix] Filtering in FIRMA

Hi, the fit() method [http://www.aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis/] takes argument 'units', which effectively defaults to units = seq_len(nbrOfUnits(cdf)). If you wish to fit only a subset of the units, you can do something like fit(plm, units=c(10:50, 540:800)) If

Re: [aroma.affymetrix] Getting error with AffymetrixCdfFile$fromChipType command

You probably meant: cdf - AffymetrixCdfFile$byChipType(HG_U95Av2) The fromChipType() method was deprecated a long time ago and eventually also removed. /Henrik On Wed, Jun 10, 2015 at 2:54 PM, anarayan gostanfordten...@gmail.com wrote: Hi, I am getting the error: Error: attempt to apply

Re: [aroma.affymetrix] doCRMAv2 vs individual normalization steps

Yes, you can use the CRMA v2 methods instead of the CRMA v1 method for these older chip types as well. The only difference is that CRMA v2 was optimized (=optimized signal-to-noise ratios) only for GenomeWideSNP_5 and forward, but all practical purposes you can use CRMA v2 for your needs. I do

Re: [aroma.affymetrix] Changing the Aroma settings (RMA MedianPolish threshold ) in the latest version of the aroma.affymetrix

tools_3.1.2 Regards, S On Thursday, June 4, 2015 at 5:31:46 PM UTC+1, Henrik Bengtsson wrote: Hi, could you please share the exact calls you are using and elaborate a bit more what makes you think it's not working? That'll help me help you. Henrik On Thu, Jun 4, 2015 at 6:40 AM

Re: [aroma.affymetrix] Changing the Aroma settings (RMA MedianPolish threshold ) in the latest version of the aroma.affymetrix

Hi, could you please share the exact calls you are using and elaborate a bit more what makes you think it's not working? That'll help me help you. Henrik On Thu, Jun 4, 2015 at 6:40 AM, sanjana sood.sanj...@gmail.com wrote: Hi, Our group is working with HTA platform and using

Re: [aroma.affymetrix] cfit error while doCRMAv2

to have the exact same genomic location. This is a warning I cannot do anything about, but again, it's harmless. Henrik Thanks so much! Arshi On Friday, May 29, 2015 at 7:35:13 PM UTC-4, Henrik Bengtsson wrote: BTW, the output of packageDescription(sfit) is also useful

Re: [aroma.affymetrix] cfit error while doCRMAv2

BTW, the output of packageDescription(sfit) is also useful for troubleshooting - it will particularly tell you when and for what version of R it was build and installed. /Henrik On Fri, May 29, 2015 at 4:33 PM, Henrik Bengtsson h...@aroma-project.org wrote: This all looks good, so it's

Re: [aroma.affymetrix] cfit error while doCRMAv2

a namespace (and not attached): [1] matrixStats_0.14.0 digest_0.6.8 R.huge_0.9.0 PSCBS_0.44.0 [5] splines_3.2.0 tools_3.2.0R.cache_0.10.0 base64enc_0.1-2 [9] aroma.apd_0.6.0tcltk_3.2.0 On Friday, May 29, 2015 at 3:17:18 PM UTC-4, Henrik Bengtsson wrote: First

Re: [aroma.affymetrix] extract LRR and BAF from ACNE results

So, there are few things here: 1. In the Aroma Framework, we always try to store estimates/signals on the original scale, e.g. even if, say, chip-effect estimates are original on the log scale, we unlog those before saving. That is a policy with the rationale that all data can always be

Re: [aroma.affymetrix] Adjusting for sample-specific median signal prior to segmentation

[Reposting from an approved email address] Hi Benilton, The locus level (total) CN ratios passed to CBS is simply the log2(T/R), where 'T' is the total CN signal (no ratio) for sample T (tumor say) and 'R' is ditto for the reference used to standardize (aka normalize by some books). Typically,

Re: [aroma.affymetrix] Error when calling doCRMAv2

It's a known bug (due to a single newline added by mistake) in aroma.affymetrix 2.13.0. Fixed in 2.13.1. Update by: source('http://callr.org/install#aroma.affymetrix') and you should be ready to go. /Henrik On Fri, Mar 13, 2015 at 11:35 AM, Georg wzz150...@gmail.com wrote: Hi There, I am

Re: [aroma.affymetrix] annotation file update

Hi. See Section 'Aroma-specific annotation files' at http://aroma-project.org/howtos/ for how tos on updating UGP and UFL. Those subpages have straightforward/detailed instructions how to import from NetAffx files. Please consider sharing your generated files; we're happy to host. Cheers,

Re: [aroma.affymetrix] Re: strange result from PSCBS

there are three but there are only two bands in the normal sample(see attachment). The tumor sample looks okey. Br, Chengyu On Wednesday, February 25, 2015 at 10:36:10 PM UTC+2, Henrik Bengtsson wrote: Hi, it's not easy to say. My point is that you look at the normal data, i.e. BAF (but also

Re: [aroma.affymetrix] Re: strange result from PSCBS

. But not sure whether I should leave this sample out for alteration calls. You are expert of PSCBS, can you give me suggestion here? Br, C.Y On Monday, February 23, 2015 at 9:54:47 PM UTC+2, Henrik Bengtsson wrote: Hi, DH signals are only defined for heterozygous SNPs, so lack of DHs

Re: [aroma.affymetrix] Re: strange result from PSCBS

UTC+2, Henrik Bengtsson wrote: DH is only defined from heterozygous SNPs. If you don't see any DH signals, that indicates that none of the SNPs where called heterozygous. This could be an indicatation of a failed or a very noise normal sample. /Henrik -- -- When reporting problems

Re: [aroma.affymetrix] Re: strange result from PSCBS

DH is only defined from heterozygous SNPs. If you don't see any DH signals, that indicates that none of the SNPs where called heterozygous. This could be an indicatation of a failed or a very noise normal sample. /Henrik -- -- When reporting problems on aroma.affymetrix, make sure 1) to run

Re: [aroma.affymetrix] Errors occurred in the PSCBS analysis

I'll try to catch up with a few questions; comments below. On Mon, Feb 9, 2015 at 3:52 AM, Chengyu Liu chengyu.liu...@gmail.com wrote: Hi, I am doing allele-specific analysis using PSCBS package. I have paired tumor-normal matched samples. For one of the samples, i got an error which is like

Re: [aroma.affymetrix] fit CBS model error

: It worked! I did load the annotation package and hgu133a for other analysis. Couldt be some name space collision. Restarting seems to work. Now it had passed that error and running... Thanks again very much! Jerry On Monday, January 26, 2015 at 11:32:25 AM UTC-5, Henrik Bengtsson wrote: On Mon

Re: [aroma.affymetrix] Questions on extracting probeset summaries

an explicit test on creating and re-creating monocell CDF. On Fri, Jan 23, 2015 at 8:49 AM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: I managed to reproduce this now: Error in (...) : 3 arguments passed to '(' which requires 1 20150123 08:48:49| Could not locate monocell CDF. Will create

Re: [aroma.affymetrix] Questions on extracting probeset summaries

This is odd for several reasons, e.g. I'm puzzled how you ended up with a monocell CDF previously but now it gives an error. Let's troubleshoot more... What does troubleshoot() output directly after you get that error? Henrik On Jan 23, 2015 7:23 AM, Qingzhou Zhang zqznept...@gmail.com wrote:

Re: [aroma.affymetrix] Questions on extracting probeset summaries

On Jan 23, 2015 7:36 AM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: This is odd for several reasons, e.g. I'm puzzled how you ended up with a monocell CDF previously but now it gives an error. Let's troubleshoot more... What does troubleshoot() output directly after you get that error? I

Re: [aroma.affymetrix] Questions on extracting probeset summaries

is the traceback() 1: extractDataFrame(ces, units = NULL, addNames = TRUE) I tried several times, but always got a data frame containing 27604 obj. :-( Thanks On Friday, 23 January 2015 01:36:00 UTC+8, Henrik Bengtsson wrote: On Thu, Jan 22, 2015 at 5:44 AM, Qingzhou Zhang zqzne...@gmail.com

Re: [aroma.affymetrix] Re: Regarding the copy number states and further processing

Hi guys, here are some late feedback on this discussion: * When talking about copy numbers, it is important to always be very clear and distinguish between whether we talk about normal/germline CNs or tumor CNs. The former take integer CN levels (0, 1, 2, 3, ...), whereas for tumors we very

Re: [aroma.affymetrix] Questions on extracting probeset summaries

On Thu, Jan 22, 2015 at 5:44 AM, Qingzhou Zhang zqznept...@gmail.com wrote: Hi Henrik, I was processing HG-U133_Plus_2 datasets. While extracting probeset summaries(chip effects) as a data frame, I only got 27604 objs * n variables. I was hoping to get a data frame of 54675 objs., which

Re: [aroma.affymetrix] sfit

It seems as you don't have the 'sfit' package installed. Not sure how you installed aroma.affymetrix in the first place (the recommended way is shown at http://aroma-project.org/install/), but try: source('http://callr.org/install#sfit') That should install 'sfit'. If the installation of

Re: [aroma.affymetrix] Is it necessary to update annotation files (CytoscanHD array)

Hi. The Aroma Cell Sequence (ACS) file does not have to be updated, since it only contains the probe sequences on the array and those never changes. The Unit Genome Position (UGP) file specifies the (chr, pos) genomic coordinates for the probe sets, which depends on the genome reference/build.

Re: [aroma.affymetrix] Could not loacate CystoScanHD_Array annotation

+2, Henrik Bengtsson wrote: On Mon, Dec 15, 2014 at 8:38 AM, Chengyu Liu chengyu...@gmail.com wrote: Thanks. I tried to bypass the NetAffx issue. I downloaded the cdf file from aroma ( http://www.aroma-project.org/data/annotationData/chipTypes/CytoScanHD_Array/) and Affymetrix website

Re: [aroma.affymetrix] RmaBackgroundCorrection: error on v4-to-v3-converted HuEx-1_0-st-v2 CEL file

again. Aisyah On Saturday, January 3, 2015 7:53:13 AM UTC+8, Henrik Bengtsson wrote: I fail to reproduce this with R 3.0.2 and affxparser 1.34.4 and aroma.affymetrix_2.12.8 and the same data file (just like you). However, from code inspection it could be that you have some cached results

Re: [aroma.affymetrix] RmaBackgroundCorrection: error on v4-to-v3-converted HuEx-1_0-st-v2 CEL file

here http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-181/samples/ BT549 is the 8th row from the top I think. Best Aisyah On Tuesday, December 30, 2014 9:11:26 AM UTC+8, Henrik Bengtsson wrote: It turns out this error is triggered inside affxparser::updateCel() and it looks like

Re: [aroma.affymetrix] RmaBackgroundCorrection: error on v4-to-v3-converted HuEx-1_0-st-v2 CEL file

| Array #1 ('EA_BT549') of 1...done 20141229 05:17:59|Background correcting data set...done As a result, no csBC object is created. Aisyah On Tuesday, December 30, 2014 6:55:59 AM UTC+8, Henrik Bengtsson wrote: On Mon, Dec 29, 2014 at 1:37 PM, Amon aisy...@gmail.com wrote: Hello

Re: [aroma.affymetrix] Encountered ERROR while extracting chip effects

, December 10, 2014 11:39:50 PM UTC+2, Henrik Bengtsson wrote: Hi, you cannot use RMA on exon-arrays, you will need to use exon-aware method such as FIRMA (e.g. http://aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis). Hope this helps Henrik PS. For http://aroma-project.org

Re: [aroma.affymetrix] Encountered ERROR while extracting chip effects

Hi, you cannot use RMA on exon-arrays, you will need to use exon-aware method such as FIRMA (e.g. http://aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis). Hope this helps Henrik PS. For http://aroma-project.org/replication/RMA, I've updated it to use `theta - extractTheta(ces)`

Re: [aroma.affymetrix] using custom CDF file in aroma.affymetrix

I downloaded the two non-official CDFs * HTA-2_0.r1.exon.cdf * HTA-2_0.r1.gene.cdf from http://www.affymetrix.com/support/technical/byproduct.affx?product=human_transcriptome. I then renamed them to use commas instead of periods for the tags. When I inspect them I see that they report an array

Re: [aroma.affymetrix] using custom CDF file in aroma.affymetrix

This looks all correct to me. What is your sessionInfo() after receiving this error? /Henrik On Wed, Oct 15, 2014 at 4:19 AM, sanjana sood.sanj...@gmail.com wrote: Hi, I am using a Custom cdf file HTA-2_0,Transcript,binary.cdf in aroma. affymetrix to analyse HTA-2_0 chip . I am using the

Re: [aroma.affymetrix] [process and display function in aroma.affymetrix]

points: 6515x8 5000x1 See 'models/RmaPlm/skipThreshold' on http://aroma-project.org/settings /Henrik Thanks again, Best Sunghee 2014년 9월 21일 일요일 오전 1시 46분 6초 UTC+9, Henrik Bengtsson 님의 말: How are you setting up the ArrayExplorer? It looks like you're missing to set the color

Re: [aroma.affymetrix] [process and display function in aroma.affymetrix]

, Henrik Bengtsson 님의 말: On Fri, Sep 19, 2014 at 8:24 AM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: Sorry, it took me a while to spot the actual problem; display(ae) The file /foo/arom-anal/\foo\arom-anal\reports\tissues\RBC,QN,RMA\ArrayExplorer.html does not exist. (I'm surprised

Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)

JikJi Daero Heung Deok Gu Cheng Ju City Chung Buk 361-841, S. Korea On Wed, Sep 17, 2014 at 2:48 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: Let's continue this off the list to spare the others the noise and post back when we found the solution. Continuing, and before I'll have

Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)

at 11:11 PM, jjspring OH sshshoh1...@gmail.com wrote: Finally working well after changing into one step further deeper directory as your comment, Sunghee 2014년 9월 17일 수요일 오후 3시 2분 20초 UTC+9, Henrik Bengtsson 님의 말: (Back to the public forum) REPRODUCIBLE EXAMPLE: It's a bug (still

Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)

That is really odd and I've never seen that error (8-9 years now). There must be a simple answer to this. What does: print(plm) print(getwd()) output when you get to that step. /Henrik On Tue, Sep 16, 2014 at 9:38 PM, jjspring OH sshshoh1...@gmail.com wrote: Hi, After setting up the

Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)

UTC+9, Henrik Bengtsson 님의 말: That is really odd and I've never seen that error (8-9 years now). There must be a simple answer to this. What does: print(plm) print(getwd()) output when you get to that step. /Henrik On Tue, Sep 16, 2014 at 9:38 PM, jjspring OH sshsh...@gmail.com wrote

Re: [aroma.affymetrix] Errors on setup working directory

Note that there should be/is a comma after the chip type prefix 'RaGene-1_0-st-v1', so rename that 'RaGene-1_0-st-v1.r3.cdf' to 'RaGene-1_0-st-v1,r3.cdf' and retry. You find some information on this in http://aroma-project.org/setup/annotationData and illustrated in

Re: [aroma.affymetrix] Error when analyzing CEL files using process() function: No permission to modify existing file: /probeData...

I've updated aroma.affymetrix v2.11.8 and friends. Update by: source(http://callr.org/install#aroma.affymetrix;) I'd be keen to hear whether this solves your problem or not. /Henrik On Thu, Sep 4, 2014 at 1:47 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: Hi, good that it works for you

Re: [aroma.affymetrix] Error when analyzing CEL files using process() function: No permission to modify existing file: /probeData...

code from the aroma repo. Thanks for your help with this and for taking a look at the issue so quickly. Best regards, Taylor On Thursday, September 4, 2014 1:37:36 PM UTC-4, Henrik Bengtsson wrote: Hi, interesting. A quick guess is that the input file, i.e. rawData/NIK_2014

Re: [aroma.affymetrix] normalization running for long time (3 weeks)

Hi. On Tue, Jun 24, 2014 at 8:45 AM, rafi...@gmail.com wrote: Hello, I have a large dataset of ~1 CEL files that needs to be normalized. I tried using aroma.affy for this, but the job is running for more than 3 weeks and in need of help/suggestions. The data is in standard affy rat2302

Re: [aroma.affymetrix] read in CEL.gz files

Hi, slow response but answers below. On Wed, Apr 2, 2014 at 8:20 AM, hr hr...@nyu.edu wrote: Dear Henrik, Is there a way to read in CEL.gz files rather than .CEL files? Unfortunately not, only non-compressed CEL files are supported. This is mainly because the Affymetrix Fusion SDK that we

Re: [aroma.affymetrix] NA values in aroma.affymetrix

Hi, considered that there are lots and lots of functions in aroma.affymetrix your questions is a bit vague, but if your thinking of missing values in probe signals, then yes, such probes are ignored and won't affect the estimates. /Henrik On Sun, May 25, 2014 at 9:50 AM,

Re: [aroma.affymetrix] CYTOSCAN HD Analysis using PSCBS

Hi. On Fri, May 16, 2014 at 1:23 AM, Farhan Haq farhanh...@gmail.com wrote: Hello, I have two questions regarding cnv analysis using CytoscanHD data. 1) I am currently implementing PSCBS on my Cancer datasets. This tool looks quite interesting to me. However, what to do you say about

Re: [aroma.affymetrix] Doubts in PSCBS segments

vignette. Best Juanjo El martes, 15 de abril de 2014 18:43:42 UTC+2, Henrik Bengtsson escribió: Hi, from the script you attached I see that you're looking at the online vignette http://aroma-project.org/vignettes/PairedPSCBS-lowlevel FYI, there is also a vignette in the PSCBS package [e.g

Re: [aroma.affymetrix] Doubts in PSCBS segments

lunes, 14 de abril de 2014 23:51:20 UTC+2, Henrik Bengtsson escribió: Hi, agree, that certainly doesn't look correct - but there's probably a simple explanation/fix. Before anything else, what version of PSCBS are you running, i.e. what's your sessionInfo(). Also, exactly what does you script

Re: [aroma.affymetrix] R library Feature addition/requests

Hi, this sounds interesting. Could you elaborate a bit more on what you are trying to do/achieve? A background may also help understand and help to help you. Cheers, Henrik On Thu, Apr 3, 2014 at 1:07 PM, Dan Wlodarski dan.wlodar...@gmail.com wrote: To whom it may concern: I'm a PhD

[aroma.affymetrix] aroma.affymetrix v2.12.0 released

Hi, aroma.affymetrix v2.12.0 has been released and is available on CRAN (where the package is hosted). Update by: source(http://aroma-project.org/hbLite.R;) hbInstall(aroma.affymetrix) This update contains a few bug fixes (thanks for the reports), a few speedups plus some small bells and

Re: [aroma.affymetrix] Speeding up RmaBackgroundCorrection

/ImproveProcessingTime /Henrik Best, Damian On Tuesday, March 4, 2014 8:32:17 PM UTC-5, Henrik Bengtsson wrote: Did lowering memory/ram solve your problem? Also, an updated version of affxparser that no longer should overflow by the integer multiplication is available (on Bioconductor). Cheers

Re: [aroma.affymetrix] Speeding up RmaBackgroundCorrection

Did lowering memory/ram solve your problem? Also, an updated version of affxparser that no longer should overflow by the integer multiplication is available (on Bioconductor). Cheers, Henrik On Thu, Feb 27, 2014 at 12:36 PM, Henrik Bengtsson henrik.bengts...@aroma-project.org wrote

Re: [aroma.affymetrix] parallel computing with aroma copy number segmentation

-5, Henrik Bengtsson wrote: Hi. On Thu, Dec 2, 2010 at 10:24 AM, Kai wang...@gmail.com wrote: Hi Henrik, I was trying to run segmentation on a large set of ~300 SNP genotyping array profiles. Currently I am loading all the profiles into aroma and run the segmenter on them one by one

Re: [aroma.affymetrix] Re: passing parameters to glad()

On Fri, Feb 21, 2014 at 3:43 AM, Hans-Ulrich hans-ulrich.kl...@uni-muenster.de wrote: Hi, I went through the code today and removed two lines from the function segmentByGLAD() from the arome.core package (version 2.11.0): # Cleaning out unknown parameters # keep - (names(params) %in%

Re: [aroma.affymetrix] Speeding up RmaBackgroundCorrection

DNAcopy_1.35.1 [5] PSCBS_0.40.4R.cache_0.9.2 R.huge_0.6.0R.rsp_0.9.28 [9] tools_3.0.2 On Thursday, February 20, 2014 1:21:25 PM UTC-5, Henrik Bengtsson wrote: On Tue, Feb 18, 2014 at 7:30 PM, Damian Plichta damian@gmail.com wrote: Thanks, that helped a lot. It took me less

Re: [aroma.affymetrix] Re: QC analysis and HuEx

, with a handful of files), run your entire script and report back. Cheers, Mark On 25-Feb-10, at 8:19 AM, Henrik Bengtsson wrote: Ok, before we try to troubleshoot this one, please update to the latest aroma.affymetrix version. The one you are using is nearly three months old, and I

Re: [aroma.affymetrix] Re: Error in readCelHeader(pathname) : Argument 'filename' should be a single file ..

Hi, thanks for reporting with more details. I see that both of you are using aroma.core 2.11.1, and it could be that that version is causing the problem. Try to revert back to aroma.core 2.11.0 (available on CRAN) as: install.packages(aroma.core) Then restart(!) R and retry. Please let me

Re: [aroma.affymetrix] Cannot fit normalization function to enzyme error

On Tue, Jan 21, 2014 at 1:01 PM, Pierre Neuvial pierre.neuv...@genopole.cnrs.fr wrote: Hi Z., If you want people to be able to help you out, then you need to explain exactly what you did. Can you report the output of sessionInfo() and traceback(), and post a complete code example ? Have

Re: [aroma.affymetrix] Construct cdf file from pgf, clf and gene mapping file

Hi, thanks for reporting on this. On Mon, Jan 20, 2014 at 2:09 PM, Guilherme Rocha gvro...@gmail.com wrote: Dear all, Does anybody know of any good tools for constructing a cdf file from affy pgf and clf files? It appears that such tools exist: http://www.aroma-project.org/node/40 The

Re: [aroma.affymetrix] na31 x na33

Hi, I'm not sure which chip type you're working on, but if it is GenomeWideSNP_6, I've just made the na33 (hg19, dbSNP 137) UGP and UFL annotation data files available: http://aroma-project.org/chipTypes/GenomeWideSNP_6 The script used to build these files are:

Re: [aroma.affymetrix] CDF file for Human Gene 1.1 st array

On Sat, Nov 2, 2013 at 10:48 AM, jerrych...@gmail.com wrote: Hi Philip, Thank you for your reply. OK, understood. However, FYI, I have applied affyrma as well, and again I got following error. Also, I am using this binary CDF (HuGene-1_1-st-v1,byTranscript-fsetid,pd.hugene.1.1.st.v1)

Re: [aroma.affymetrix] CDF file for Human Gene 1.1 st array

On Sat, Jan 11, 2014 at 4:59 AM, ndigi...@gmail.com wrote: Hi Jerry, Have you been able to resolve this issue? I ran into the same problem while working with matlab: What's this sudden interest from the Matlab side and which Matlab toolbox is the source of all this? Warning: The ChipType

Re: [aroma.affymetrix] Re: CRMAv2 and Mapping250K_Nsp arrays

Hi, I haven't seen this before, but it certainly looks like something went wrong when aroma tried to infer the SNP nucleotide pairs for that chip type. This can either be due to issues reading the CDF or the ACS file. Before continuing, check one more time that your CDF and ACS files have

Re: [aroma.affymetrix] Hypersegmentation from Paired total copy-number analysis using CRMAv2 with GWSNP6

, according to your experience. best, Kim On Tue, Dec 17, 2013 at 11:37 PM, Henrik Bengtsson henrik.bengts...@aroma-project.org wrote: Hi. 1. It is not clear to me if you're saying that you get different results now using a newer version of aroma.affymetrix that you used before

Re: [aroma.affymetrix] Use Existing FIRMA model on new data.

Hi. On Thu, Dec 26, 2013 at 12:47 PM, Sam Danziger sam.danzi...@gmail.com wrote: I'm using FIRMA algorithm, and I would like to use an existing FIRMA model (for instance one trained on 50 arrays) on new data (e.g. 2 new arrays). I am able to train a FIRMA model (and an RMA model) quite easily

Re: [aroma.affymetrix] smoothing after CRMAv2 and before CBS?

thresholds in both cases. What to use instead? (We're working on it for the PSCBS case). For the total CN case I would use callers similar to those used by the GLAD segmentation method. Hope this helps Henrik Thanks! Emilie On Friday, December 13, 2013 4:55:26 PM UTC-5, Henrik Bengtsson

Re: [aroma.affymetrix] smoothing after CRMAv2 and before CBS?

, your tumor normal pair is not from the same patient. /Henrik Emilie On Thursday, December 12, 2013 6:01:48 PM UTC-5, Henrik Bengtsson wrote: The tumor DH panel makes me believe that either your tumor or your normal chip data is bad, or alternatively that the tumor and normal

Re: [aroma.affymetrix] smoothing after CRMAv2 and before CBS?

Pierre beat me to this one. Comments below... On Thu, Dec 5, 2013 at 9:20 AM, Pierre Neuvial pierre.neuv...@genopole.cnrs.fr wrote: Hi Emilie, OK, so you are referring to the “smooth.CNA function in the DNAcopy package, cf

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