[BioC] read.table(), then use affycoretools?
Weiyin Zhou
weiyin.zhou at exonhit-usa.com
Tue Jan 9 17:21:00 CET 2007
James,
I modified my pData.txt file, so it works now.
It is kind weird. I checked my "Apop_ram.txt", the column names are
match with row names in pData.txt. But somehow, when read.table, it
changed "-" to ".". And I did not even noticed at beginning.
Thanks a lot,
Weiyin
-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu]
Sent: Tuesday, January 09, 2007 11:05 AM
To: Weiyin Zhou
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] read.table(), then use affycoretools?
Hmm, yeah. Sorry about that. S4 and stuff ;-D
How about
a <- pData(pd)
row.names(a) <- sub("-",".", row.names(a))
pData(pd) <- a
and then proceed.
Alternatively you can modify the text file before running
read.phenoData().
Best,
Jim
Weiyin Zhou wrote:
> Hi James,
>
> Thanks!
>
> I get the error message when I try:
>
>>eset <- new("exprSet", exprs = as.matrix(data), phenoData = pd)
>
> Error in validObject(.Object) : invalid class "exprSet" object:
> sampleNames different from names of phenoData rows
>
> So I try below code, but get another error message:
>
>>row.names(pd) <- sub("-", ".", row.names(pd))
>
> Error in `rownames<-`(x, value) : attempt to set rownames on object
with
> no dimensions
>
>
> Here is my seesionInfo:
>
>>sessionInfo()
>
> R version 2.4.0 (2006-10-03)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] "splines" "tools" "methods" "stats" "graphics"
> "grDevices"
> [7] "utils" "datasets" "base"
>
> other attached packages:
> affycoretools biomaRt RCurl XML GOstats
> "1.6.0" "1.8.1" "0.8-0" "1.4-0" "2.0.4"
> Category genefilter survival KEGG RBGL
> "2.0.3" "1.12.0" "2.30" "1.12.0" "1.10.0"
> annotate GO graph limma affy
> "1.12.0" "1.14.1" "1.12.0" "2.9.1" "1.12.2"
> affyio Biobase
> "1.2.0" "1.12.2"
>
>
>
>
> Thanks,
>
> Weiyin
>
>
>
> -----Original Message-----
> From: James W. MacDonald [mailto:jmacdon at med.umich.edu]
> Sent: Tuesday, January 09, 2007 10:28 AM
> To: Weiyin Zhou
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] read.table(), then use affycoretools?
>
> Hi Weiyin,
>
> Weiyin Zhou wrote:
>
>>Hi James,
>>
>>
>>
>>I use read.table() to read .txt file, which have 7 columns (probeID, 3
>>columns for control, next 3 for ko). These data have already rma
>>pre-processed. Here is the first ten lines after I used read.table:
>>
>>
>>
>>
>>
>>>data <- read.table("Apopt_rma.txt", header=TRUE, row.names="ID")
>>
>>
>>>data[1:10,]
>>
>>
>> Eurasnet.Apoptosis.CEL Eurasnet.Apoptosis2.CEL
>>
>>AFFX-BioB-3_at 10.16030 9.75900
>>
>>AFFX-BioB-5_at 9.56744 9.07906
>>
>>AFFX-BioB-M_at 10.38530 9.94925
>>
>>AFFX-BioC-3_at 10.30660 9.81339
>>
>>AFFX-BioC-5_at 10.97160 10.54450
>>
>>AFFX-BioDn-3_at 12.43740 12.17020
>>
>>AFFX-BioDn-5_at 11.80980 11.45310
>>
>>AFFX-CreX-3_at 13.76850 13.67820
>>
>>AFFX-CreX-5_at 13.59800 13.48740
>>
>>AFFX-DapX-3_at 7.58850 8.05139
>>
>> Eurasnet.Apoptosis3.CEL Eurasnet.Apoptosis4.CEL
>>
>>AFFX-BioB-3_at 9.61602 9.43489
>>
>>AFFX-BioB-5_at 9.02821 8.83341
>>
>>AFFX-BioB-M_at 9.85227 9.69166
>>
>>AFFX-BioC-3_at 9.75543 9.62851
>>
>>AFFX-BioC-5_at 10.42980 10.27400
>>
>>AFFX-BioDn-3_at 12.00490 12.00640
>>
>>AFFX-BioDn-5_at 11.29640 11.35080
>>
>>AFFX-CreX-3_at 13.48130 13.68150
>>
>>AFFX-CreX-5_at 13.26550 13.44120
>>
>>AFFX-DapX-3_at 7.06897 6.90034
>>
>> Eurasnet.Apoptosis5.CEL Eurasnet.Apoptosis6.CEL
>>
>>AFFX-BioB-3_at 10.29660 9.69907
>>
>>AFFX-BioB-5_at 9.72952 9.08717
>>
>>AFFX-BioB-M_at 10.59420 9.92486
>>
>>AFFX-BioC-3_at 10.47480 9.89643
>>
>>AFFX-BioC-5_at 11.15980 10.54430
>>
>>AFFX-BioDn-3_at 12.58160 12.18040
>>
>>AFFX-BioDn-5_at 12.12000 11.58860
>>
>>AFFX-CreX-3_at 13.86080 13.81650
>>
>>AFFX-CreX-5_at 13.78710 13.67390
>>
>>AFFX-DapX-3_at 7.07626 7.12627
>>
>>
>>
>>My phenoData is;
>>
>>
>>
>>>pd <- read.phenoData("pData.txt", header=TRUE, row.names=1)
>>
>>
>>>show(pData(pd))
>>
>>
>> Target
>>
>>Eurasnet-Apoptosis1.CEL CO
>>
>>Eurasnet-Apoptosis2.CEL CO
>>
>>Eurasnet-Apoptosis3.CEL CO
>>
>>Eurasnet-Apoptosis4.CEL KO
>>
>>Eurasnet-Apoptosis5.CEL KO
>>
>>Eurasnet-Apoptosis6.CEL KO
>>
>>
>>
>>Can I doing some sort of conversion for the data from output of
>>read.table, to make data object look like the eset object you create
>>from affystart(), combine with phenoData info, so I can use it to call
>>lmFit () and other function in limma package.
>>
>
>
> For the current BioC release, you can create an exprSet like this:
>
> eset <- new("exprSet", exprs = as.matrix(Data), phenoData = pd)
>
> You might get an error because your phenoData row.names are not the
same
>
> as the colnames of your Data object. If so, you might have to change
the
>
> row names first.
>
> row.names(pd) <- sub("-", ".", row.names(pd))
>
> Note that this won't work with R-2.5.0/BioC 2.0. In that case you will
> have to create an ExpressionSet, and your pd object has to be read in
> using read.AnnotatedDataFrame().
>
>
> HTH,
>
> Jim
>
>
>
>
>
>>
>>
>>Thanks in advance,
>>
>>Regards,
>>
>>Weiyin Zhou
>>
>>Statistics and Data Analyst
>>
>>ExonHit Therapeutics, Inc.
>>
>>217 Perry Parkway, Building # 5
>>
>>Gaithersburg, MD 20877
>>
>>
>>
>>email: Weiyin.zhou at exonhit-usa.com
>
> <mailto:Weiyin.zhou at exonhit-usa.com>
>
>>phone: 240.404.0184
>>
>>fax: 240.683.7060
>>
>>
>>
>>
>>
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
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--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
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