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@exonhit-usa.com

phone: 240.404.0184

fax: 240.683.7060

 


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