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Hi Zaiwei,
On Sun, Dec 16, 2012 at 2:22 AM, zhouzaiwei zhouzai...@163.com wrote:
Hi , I want to apply FIRMAGene to analysis differential splicing events
of
hugene_1.0_st array and have red article (Robinson Speed, 2007) and
Perhaps something like this is what you want (note: different chip to
what you are using)?
df - readDataFrame(getCdf(cs), verbose=-80)
[...snip...]
head(df)
unit unitName unitType unitDirection unitNbrOfAtoms group groupName
11 7892501 expression sense 4 1
of intensities, but I don't know which probe
ids they correspond to. Hope this clarifies. Thanks
On Aug 9, 6:03 am, Mark Robinson markrobinson@gmail.com wrote:
Perhaps something like this is what you want (note: different chip to
what you are using)?
df - readDataFrame(getCdf(cs), verbose=-80
---
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---
Firma_Exon_question.r
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Mark Robinson
Sun, 29 Mar 2009 23:12:09 -0700
Hi Mario.
I have made some modifications to the reading of probe_tab files and
to the computing of affinities so that this procedure can run now,
either as you have done below by choosing lowly expressed probes, or
(perhaps preferably
/
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Apologies folks. Inadvertent file permissions change. It should work now.
Cheers,
Mark
-- Forwarded message --
From: vegard vegard.nyga...@medisin.uio.no
Date: Thu, Oct 21, 2010 at 2:55 AM
Subject: [aroma.affymetrix] Missing file bpmapCluster2Cdf.R in
Create a CDF from a BpMap
?
Thanks,
Qicheng
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,TisMix_mix9,28.2833712932546,ACTA1
7982090,TisMix_mix1,27.4880562975114,SNORD115-42
8103789,TisMix_mix1,27.399249112706,GPM6A
7982008,TisMix_mix1,25.0039468447955,SNORD115-1
Could you please tell me where I am wrong ?
Thanks,
Qichengm
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,
comment.char=,stringsAsFactors=FALSE)
Error in read.table(MoGene-1_0-st-v1.probe.tab, sep = \t, header =
TRUE, :
no lines available in input
I double checked the file I downloaded from Affy and it seems to be
fine!
Thx,
Daniela
On Mar 16, 4:56 pm, Mark Robinson mrobin...@wehi.edu.au wrote:
Hi
into a txt file?
Many thanks for your help.
I really appreciate it.
Daniela
On Mar 16, 4:57 pm, Mark Robinson mrobin...@wehi.edu.au wrote:
Hi Daniela.
You haven't told us what inputs you've used for 'plm' and 'cls' ...
and what is stored in 'u'?
Have you read the docs
unique CDF to the
original CDF, which obviously is curious in itself. So, a full
explanation of what you've done upstream of this would be useful.
Cheers,
Mark
On 16-Mar-10, at 1:09 AM, Henrik Bengtsson wrote:
Hi,
I leave this one to Mark Robinson who is designed createUniqueCdf
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Hi Peter.
I haven't looked at this since early 2009 and our motive in making this
available as a script (instead of within the aroma.affymetrix package) was
simply as an FYI and the code is readily available for others to modify
for their needs. You will of course understand that underlying
Hi Daniela.
Is your CDF in the:
annotationData/chipTypes/MoEx-1_0-st-v1/
directory?
(http://aroma-project.org/node/66)
Cheers,
Mark
Hi,
I stored my CDF file in annotationData/chipTypes; nevertheless I cannot
upload the file.
Can anyone please tel me what I am doing wrong:
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--is it the right one for this?
-Randy
On Jun 19 2009, 10:08 pm, Mark Robinson mrobin...@wehi.edu.au wrote:
Hi Steve.
I don't know how common this is. Basically, a colleague found agene
that was very differentially expressed when analyzing using the
Affymetrix probesets definition and found
at
http://groups.google.com/group/aroma-affymetrix?hl=en
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?
Thanks! /Libing
On Fri, Nov 6, 2009 at 6:35 AM, Mark Robinson
mrobin...@wehi.edu.au wrote:
Hi Libing.
Are you after the probe IDs from the probe.tab file? For example:
Probe IDProbe Set IDprobe x probe y assembly
seqname start stop
strand probe sequence
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dealing with ST arrays.
Thanks,
Wade
On Feb 10, 3:13 am, Mark Robinson mrobin...@wehi.edu.au wrote:
Hi Simon.
See comments below.
I am using the mouse gene ST arrays and am having problems with
annotation. When i write a csv file, theannotationis only the
probeset_id, no gene names
Hi Zaid.
There is an example flat file (well, 10 lines of it) at that page that
Pierre suggested. You'll want to filter the missing lines and make sure
all the data in a column is of the same type.
Cheers,
Mark
No.
My flat file has some lines with missing values and non integer
values.
Is
not allow it?
Thanks,
Renyi
On Sat, Dec 5, 2009 at 2:43 PM, Mark Robinson
mrobin...@wehi.edu.au wrote:
Hi Renyi.
One thing to do is check that the genome positions in your BPMAP file
for chr5 are all 0.
To do this, try:
library(affxparser)
bp - readBpmap(At35b_MR_v04
of California, Riverside
Riverside, CA 92521
Email: renyi@ucr.edu
Phone: (951)827-3987
Fax: (951)827-4437
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When reporting problems on aroma.affymetrix, make sure
$`20091119_UHR_Exon2`$out
numeric(0)
$`20091119_UHR_Exon3`
$`20091119_UHR_Exon3`$stats
[1] 0 0 0 0 0
$`20091119_UHR_Exon3`$n
[1] 18705
$`20091119_UHR_Exon3`$conf
[1] 0 0
$`20091119_UHR_Exon3`$out
numeric(0)
attr(,type)
[1] NUSE
On Nov 30, 1:28 am, Mark Robinson mrobin...@wehi.edu.au
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: plotBoxplot.ChipEffectSet(ces, type = RLE, ...)
3: plotBoxplot(ces, type = RLE, ...)
2: plotRle.QualityAssessmentModel(qamTr)
1: plotRle(qamTr)
On Nov 24, 1:50 am, Mark Robinson mrobin...@wehi.edu.au wrote:
Hi Yu Chuan.
Comments below.
On 24-Nov-09, at 1:00 PM, Yu Chuan wrote:
Hi,
I
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need
replicates. Therefore, it does not need this information.
Cheers,
Mark
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wrote:
Thanks for sharing your code.
I don't really understand - when getting the PLM for this instruction
are you supposed to set mergeGroups to true like this:
plm - ExonRmaPlm(celSet, mergeGroups=TRUE)
-L
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R.huge_0.2.0 aroma.core_1.2.0
aroma.light_1.13.6
[8] matrixStats_0.1.6 R.rsp_0.3.6R.filesets_0.5.3
digest_0.4.1 R.cache_0.2.0 R.utils_1.2.2
R.oo_1.6.2
[15] R.methodsS3_1.0.3 projectManager_1.0 XML_2.6-0
Mark Robinson wrote
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--
--~--~-~--~~~---~--~~
When
0.4552856
20.4449589
3 -0.1899892
4 -0.6681926
50.3545261
6 -0.5645628
Thanks
Hailei
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Hi Hailei.
For starters, can you give the *full* output of your sessionInfo()? The
error you are getting has something to do with the 'preprocessCore'
package and I first want to check whether it is a package version mismatch
error.
I haven't used aroma.affymetrix on R 2.10 and I don't know if
AromaPlatformInterface
AromaMicroarrayDataSet
[7] GenericDataFileSet Object
Thanks.
Hailei
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(staticMethod, args = args)
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Hi Carol.
This throws an error because your CDF has a tag (r3) and there is no way
to send a tag for the CDF file through the AffymetrixCelSet$byName
function. I recommend that you just do this in 2 commands, as you've done
successfully. Alternatively, you can remove the ,r3 from your CDF file
,] 8.038540 3.542727 3.808023 7.923751
[8,] 13.260725 6.238900 4.660217 4.200828
I have not sure what I'm doing wrong and would really appreciate any
help.
Thank you very much in advance,
Enid
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When reporting problems
Lavinia.
On Sep 1, 1:24 pm, Mark Robinson mrobin...@wehi.edu.au wrote:
Hi Lavinia.
Yes.
Bandwidth(MAT)=probeWindow(aroma.affymetrix MAT)
Also,
MinProbe(MAT)=nProbes(aroma.affymetrix MAT)
Cheers,
Mark
On 1-Sep-09, at 11:31 AM, Lavinia Gordon wrote:
Hi,
I have some older MAT pure
. Can I just check, from the MAT .tag
(parameters file), does probeWindow correspond directly to Bandwidth?
many thanks
Lavinia.
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to proceed after this step
Diya
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by:
source(http://www.braju.com/R/hbLite.R;);
hbLite(R.filesets);
library(R.filesets);
Q1) Does this work?
hbLite(aroma.core);
library(aroma.core);
Q2) Does this work?
hbLite(aroma.affymetrix);
library(aroma.affymetrix);
Q3) Does this work?
Mark (Robinson), you mentioned this problem
(in
plmData, probeData, and reports) that are created by
aroma.affymetrix?
Thanks in advance.
Kind regards,
Anbarasu
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Hi Yiwen.
I think this thread will answer your question in detail:
http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/1b0ab11fad9b4df3
In brief, the main difference is how the probe-level linear model is fit
-- median polish OR iteratively reweighted least squares with a
, and reports) that are created by aroma.affymetrix?
Thanks in advance.
Kind regards,
Anbarasu
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this with extract(). For example, say 'cs' is an
AffymetrixCelSet object. You can extract the first 2 samples with:
csSubset - extract(cs, 1:2)
Hope that helps.
Mark
Thank you very much.
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Hi Naresh.
That particular script (flat2Cdf.R) creates a PM-only CDF.
But, if you understand the format of a CDF file -- you might read in the
your original CDF with readCdf() from the 'affxparser' package to
understand it -- then you should be able to modify the script to include
MM probes.
by using windows, you could alternatively
install the cygwin tools and then have access to the standard battery
of command line tools, such as grep/awk from the example.
Cheers,
Mark
regards,
John
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Hi Lars.
Apologies for the slow response.
I do have some scripts for calling enriched regions, but they are not
really ready for public consumption. And, they are geared more towards
ChIP-chip of modified histones / DNA methylation than either TF binding or
transcript expression. We have
.
Regards,
-Steve
On Jun 17, 9:56 am, Steve Piccolo steve.picc...@gmail.com wrote:
Yesterday I posted this question to the list, but the spam blocker
didn't
let it through. Below my question is a response from Mark Robinson
, Apr 11, 2009 at 5:48 PM, Mark Robinson
mrobin...@wehi.edu.au wrote:
Hi Libing.
As the error message suggests, there are no degrees of freedom for the
fit, meaning you have no replicates. It appears you only have 2 total
samples, one for each group. You wouldn't be able to use limma to do
,
Nick
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, 12:32 am, Mark Robinson mrobin...@wehi.edu.au wrote:
Hi Sabrina.
How about you try and create a 'flat' file like the one described
at:http://groups.google.com/group/aroma-affymetrix/web/creating-cdf-file
...
Presumably, you will be comfortable with the Exon Array's 'probetab'
file
.
Or, if you could direct me to some document that would tell me how to
build custom cdfs, that would be good too.
Thanks very much,
Dick
On Aug 4 2008, 10:05 pm, Mark Robinson mrobin...@wehi.edu.au wrote:
Hi folks.
I've been updating/creating CDF files for some of the recent
Affymetrix whole
.
Cheers,
Mark
Sabrina
On Apr 30, 3:46 am, Mark Robinson mrobin...@wehi.edu.au wrote:
Hi Sabrina.
I have not had to deal with this myself, but I do know that it
exists
and I can at least suggest a possible route to exclude affected
exons.
Presumably, there is a database (dbSNP
am, Mark Robinson mrobin...@wehi.edu.au wrote:
Hi Sabrina.
I have not had to deal with this myself, but I do know that it exists
and I can at least suggest a possible route to exclude affected
exons.
Presumably, there is a database (dbSNP?) that tells you the genome
locations of each SNP
Hi Ettore.
Comments below.
I have the following question. In the sup3.R file the probe level
model fitting is realised using the instructions:
plm - RmaPlm(csNU)
fit(plm, verbose=verbose)
where csNU is an object obtained after background correction, quantile
normalisation and
special mouse Exon array CDF files... any advice on how I can
get hold of them?
Thanks
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23153762 35
6 2315373 23153772 46
What does each column, especially the unitName and groupName mean ?
And how can I correlate unitName and groupName to gene name and exon
number? Thanks in advance!
Xinjun
On Thu, Apr 30, 2009 at 3:31 PM, Mark Robinson
row corresponds to. I'm
guessing here, but you are probably interested in the YRIvsCEU
parameter, so you'd probably sort on the p.value.YRIvsCEU column ...
Cheers,
Mark
On Tue, Apr 28, 2009 at 4:29 PM, Mark Robinson
mrobin...@wehi.edu.au wrote:
Hi Xinjun.
Comments below
with SNP data before, can anyone give me a hint? Thanks a
lot!
Sabrina
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here. The probesets where the Grp2
coefficient is significantly different from 0 may highlight
differentially spliced exons. Does that help?
Mark
Thanks in advance!
Xinjun
On Mon, Apr 27, 2009 at 6:19 AM, Mark Robinson
mrobin...@wehi.edu.au wrote:
Hi Xinjun.
Quick comments
Mitchell
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: system.time({
writeCdf(outFilename, cdfheader = cdfHeader, cdf = cdfUnits,
cdfqc = cdfQcUnits, overwrite = TRUE, verbose = verbose2)
})
1: convertCdf(files[kk], outFiles[kk], version = 4, force = TRUE,
verbose = TRUE)
On Sat, Apr 25, 2009 at 4:37 PM, Mark
,
Mark
On 01/04/2009, at 6:25 AM, jing ma wrote:
Dear Mark,
When doing background subtraction for the Affy exon array, do you
think it is sufficient to use the CORE CDF (I usually use HuEx-1_0-
st-v2,coreR3,A20071112,EP.cdf)?
Thanks,
Jing
On Mon, Mar 16, 2009 at 5:35 PM, Mark Robinson
where TRUE/FALSE needed
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wondering if writeCel() is the one I should use. There are no
documents for its usage. Can anyone provide more details? Or some
links. Thanks!
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Hi Jake.
As a starting point, you might have a look at:
http://groups.google.com/group/aroma-affymetrix/web/creating-cdf-files-from-scratch
In there is a script called 'flat2Cdf.R' that takes a flat file of probe
information (X/Y location on the chip, probe sequence, identifiers) and
creates a
/1b0ab11fad9b4df3/f745ed0860546313
But, I'd be interested to hear more details if you do look into it more.
Cheers,
Mark
Best regards
Christian
On Mar 16, 9:13 am, Mark Robinson mrobin...@wehi.edu.au wrote:
Hi Christian.
From what I can tell looking at your code (rather quickly, i must
admit
?
GenomeGraphs_ENSG0060237.pdfGenomeGraphs_ENSG0060237.R
--
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robin...@garvan.org.au
e: mrobin...@wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
.
The reason is that I want to process these CEL files together,
however I don't want to copy them to one folder.
Thanks.
--
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robin...@garvan.org.au
e: mrobin...@wehi.edu.au
p: +61 (0)3 9345
this to the BioC
mailing list instead?
thanks for your help,
Sebastien
--
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robin...@garvan.org.au
e: mrobin...@wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
--
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robin...@garvan.org.au
e: mrobin...@wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
--
--~--~-~--~~~---~--~~
When reporting
--
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robin...@garvan.org.au
e: mrobin...@wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
--
--~--~-~--~~~---~--~~
When reporting problems
Hi Sebastien.
Note that plotRle() eventually makes a call to 'bxp' (in the graphics
package that is loaded by default) and any/all arguments are passed on.
Have a look at ?bxp for what you can specify.
For example:
[...]
qamTr - QualityAssessmentModel(plmTr)
plotRle(qamTr,
() is: 1535.875
Does anyone have any suggestion to solve this problem? Thanks!!!
Sabrina
--
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robin...@garvan.org.au
e: mrobin...@wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
(nProbesPerExon)
Thanks and Have a great weekend
Sabrina
On Jan 22, 5:18 pm, Mark Robinson mrobin...@wehi.edu.au wrote:
Hi Sabrina.
See below.
On 23/01/2009, at 3:17 AM, sabrina wrote:
Hi, Mark:
Thanks for the suggestions. I think I will go with one of the
replicates for now
these rows before you use lmFit().
Cheers,
Mark
Thanks!
Sabrina
On Jan 20, 7:48 pm, Mark Robinson mrobin...@wehi.edu.au wrote:
Hi Sabrina.
Do you have biological replicates of some samples and technical
replicates of others? Or, just technical replicates of everything?
My experiment
would be greatly appreciated.
Thanks.
Anbarasu
--
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robin...@garvan.org.au
e: mrobin...@wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
Hi Sabrina.
Do you have biological replicates of some samples and technical
replicates of others? Or, just technical replicates of everything?
My experiment has two groups, one has 5 samples (biological
replicates, that is 5 mice from one strain), and the other has 4
samples. Among 5
!
Sabrina
--
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robin...@garvan.org.au
e: mrobin...@wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
looks good.
Pairs plots
are attached.
Thanks,
Peter
On Thu, Dec 4, 2008 at 5:41 PM, Mark Robinson
mrobin...@wehi.edu.au wrote:
Thanks Peter.
Perhaps you can repeat this comparison after the next release (this
will be very soon!) and split the aroma.affymetrix comparison
.
Thanks,
Anguraj
--
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robin...@garvan.org.au
e: mrobin...@wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
get decent normalization between batches. Is there a way to
adjust for batch effects in aroma.affy that can be incorporated into
an exon array analysis?
Thank you,
Sarah
--
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robin
of
samples ...
Thanks for all these questions Sabrina. This will help make a nice
vignette ... when I get time :)
Unless you'd be interested in summarizing your approach! :)
Cheers,
Mark
Sabrina
On Dec 9, 5:02 pm, Mark Robinson [EMAIL PROTECTED] wrote:
Hi Sabrina.
Great work! See below
need to create or download your mogene10stv1cdf library
from
the Affy unsupported CDF file (https://stat.ethz.ch/pipermail/bioc-
devel/2007-October/001403.html has some detail on how to do this).
However, as Mark Robinson pointed out there are potential issues with
using the Affy unsupported
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