[BioC] read.table(), then use affycoretools?
Weiyin Zhou
weiyin.zhou at exonhit-usa.com
Tue Jan 9 16:56:08 CET 2007
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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