[BioC] read.table(), then use affycoretools?

[James W. MacDonald]

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
> 
>  
> 
>  
> 
>  
> 
> 
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> 
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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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