[aroma.affymetrix] RE: PdInfo2Cdf function

Biostrings_2.15.27 IRanges_1.5.79 [4] preprocessCore_1.9.0 splines_2.11.0 tools_2.11.0 -Original Message- From: aroma-affymetrix@googlegroups.com [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Hooiveld, Guido Sent: 21 April 2010 21:08 To: 'Mark Robinson

[aroma.affymetrix] bug in function pdInfo2Cdf

Dear Henrik, I would like to report a problem with the function pdInfo2Cdf.R I know this function is not part of the core functionality of aroma.affymetrix, but i thought it still would be good to inform you about the error i found. Meanwhile I found out it is caused by line 71: the argument

RE: [aroma.affymetrix] Re: writeCdf.AffyGenePDInfo Error in order(u$atom): argument 1 is not a vector

Hi, In addition to Henrik's remarks, I also would like to comment: - Entrez Gene-based remapped CDFs (the ones from MNBI) are normally used for the analyses fo expression arrays; the array type you would like to analyse is not such an array! That's the reason the coverage is so little! - you

RE: [aroma.affymetrix] Gene 2.0 ST arrays

Hi, To follow up on Henrik's suggestion: we recently have made Bioconductor-compatible ('unofficial') CDFs for the STv2.0/2.1 arrays as well, essentially using the PD.Info packages. Please find them here: http://nmg-r.bioinformatics.nl/ HTH, Guido -Original Message- From:

RE: [aroma.affymetrix] Gene 2.0 ST arrays

, Dec 7, 2012 at 5:21 AM, Hooiveld, Guido guido.hooiv...@wur.nl wrote: Hi, To follow up on Henrik's suggestion: we recently have made Bioconductor-compatible ('unofficial') CDFs for the STv2.0/2.1 arrays as well, essentially using the PD.Info packages. Please find them here: http://nmg

[aroma.affymetrix] Error in if (hasTimestamp) { : argument is of length zero

Hi Henrik, I am testing the binary CDF files I created for various Gene ST arrays (re: discussion last Friday), but I run into problems. An error is occurring when reading the cell files. According to the change log this error has been reported before and should have been fixed by you (in

[aroma.affymetrix] binary CDF files on-line

Hi all, This is to inform you that (finally) we have put on-line the binary CDFs for 18 arrays. Please find them on our server (Table 4): http://nmg-r.bioinformatics.nl/NuGO_R.html CDFs are available for these arrays: AraGene-1_0-st AraGene-1_1-st HuGene-1_0-st-v1 HuGene-1_1-st-v1 HuGene-2_0-st

RE: [aroma.affymetrix] Re: Gene 2.0 ST arrays

Hi, You can obtain a set of sample HuGene 2.0 arrays directly from Affymetrix: http://www.affymetrix.com/support/downloads/demo_data/human2_0.zip Regards, Guido From: aroma-affymetrix@googlegroups.com [mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Neetu Tandon Sent: Wednesday, February

RE: [aroma.affymetrix] Re: Gene 2.0 ST arrays

if i get a dataset listed in GEO or ArrayExpress for testing my analysis method. Is it possible that none of the publicly available datasets use this platform? Thanks and Regards, Neetu On Wed, Feb 20, 2013 at 2:29 PM, Hooiveld, Guido guido.hooiv...@wur.nlmailto:guido.hooiv...@wur.nl wrote: Hi

RE: [aroma.affymetrix] gene-centric CDF for HT HG U133A arrays (TCGA GBM data)

Hi, Did you check the website of the MBNI folks? AFAIK Manhong Dai et al offer remapped (custom) CDFs for this array type (and many others) in various flavors (e.g. based on ENSEMBL gene/transcript, NCBI Entrez Gene / RefSeq, etc.)

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

Hi, I was a little curious to know what these scripts are able to construct/convert, so I had a quick look at the codes. @ Elizabeth (or others): Although I am not planning to use these (yet), there is one thing that (naively?) did not become immediately clear to me: what is the expected content

RE: [aroma.affymetrix] AffymetrixCdfFile$byChipType -- Argument 'nbrOfUnits' contains 1 NA value(s)

Hi, Creating the CDF object using the same binary CDF file works fine in my hands… ?? See below. It has been a while since I extensively used aroma.affymetrix, but I noticed the main difference between your and my code is that you specifically set in R all relevant directories (cel.directory,