[BioC] Agilent's one color array

[Weiyin Zhou]

It works.  Thanks, Weiwei.

Weiyin

-----Original Message-----
From: Weiwei Shi [mailto:helprhelp at gmail.com] 
Sent: Thursday, June 14, 2007 4:36 PM
To: Weiyin Zhou
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Agilent's one color array

can you just use

newData = as.matrix(data[, 2:5])

rownames(newData) = data[, 1]


So your rownames contain ID you need.

HTH,

Weiwei

On 6/14/07, Weiyin Zhou <weiyin.zhou at exonhit-usa.com> wrote:
> Dear listers,
>
>
>
> I am analyzing Agilent's one-color array.  I use limma package to read
> data then do quantile normalization between arrays on RG$G and log2
the
> data.   Then I try to convert the data  to exprSet object so I can
> analyzing it the way similar to Affmetrix array.
>
>
>
> > data[1:5,]
>
>              ID File1 File2 File3 File4 File5 File6
>
> 1 A_15_P100001  9.92  9.91  9.86 10.07 10.03  9.86
>
> 2 A_15_P100002  9.40  9.20  8.81  8.82  8.89  8.94
>
> 3 A_15_P100003  4.08  3.67  3.32  2.47  2.89  2.91
>
> 4 A_15_P100004  2.30  2.41  2.51  2.81  2.68  2.57
>
> 5 A_15_P100005 11.29 11.38 11.25 10.94 11.06 11.29
>
>
>
> > pd <- read.phenoData("pData.txt", header=TRUE, row.names=1)
>
> > show(pData(pd))
>
>       Target
>
> File1 group1
>
> File2 group1
>
> File3 group1
>
> File4 group2
>
> File5 group2
>
> File6 group2
>
>
>
> > eset <- new("exprSet", exprs = as.matrix(data), phenoData = pd)
>
> Error in validObject(.Object) : invalid class "exprSet" object: 1:
> number of exprs columns different from number of pData rows
>
> invalid class "exprSet" object: 2: sampleNames different from names of
> phenoData rows
>
>
>
> I know the problem is because the ID column.   Is there any way I can
> only read data starting from second column(File1) but also associate
the
> result with ID later on?
>
>
>
> > 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:
>
>    biomaRt      RCurl        XML    GOstats   Category genefilter
> survival
>
>    "1.8.1"    "0.8-0"    "1.4-0"    "2.0.4"    "2.0.3"   "1.12.0"
> "2.30"
>
>       KEGG       RBGL   annotate         GO      graph       affy
> affyio
>
>   "1.12.0"   "1.10.0"   "1.12.0"   "1.14.1"   "1.12.0"   "1.12.2"
> "1.2.0"
>
>    Biobase      limma
>
>   "1.12.2"    "2.9.1"
>
>
>
>
>
> Thanks in advance,
>
>
>
> Weiyin
>
>
>
>
>
>
>
> Weiyin Zhou
>
> Senior Research Associate
>
> ExonHit Therapeutics, Inc.
>
> 217 Perry Parkway, Building # 5
>
> Gaithersburg, MD 20877
>
>
>
> email: Weiyin.zhou at exonhit-usa.com
>
> phone: 240.404.0184
>
> fax: 240.683.7060
>
>
>
>
>         [[alternative HTML version deleted]]
>
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>


-- 
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

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