[BioC] CELfiles names in a matrix

[Joshi, Nina (NIH/NCI)]

I am uploading cel files with the command justRMA.  I create a phenoData
file first using:

 

pD1 <-  read.phenoData(filename="phenodata.txt, header = T, sep="\t')  

 

note: phenodata.txt is a text file with variables in columns and samples
number and/or names in rows.  The output file appears to have the correct
number of cases (133) and variables (20)

 

Then I create a file, x, that has all the CEL file names.

 

Then I attempt to create a Affybatch using justRMA:

 

Data1 <- justRMA (sampleNames=x, phenoData=pD1)

 

The output file, a matrix, opened in excel has the correct number of CEL
files listed in columns (133 cases) and the correct number of genes listed
in rows, but the columns are shifted to the left.  They are numbered x1, x2,
x3...with the first column, the gene name, numbered as x1 and the last
column, data from a CEL file, left blank.  I want the columns named with CEL
file names and the first column names "gene names".  What is the code to do
this?  

 

Thanks,

 

Nina 

             

 

Nina Joshi, PhD

NIH/NCI/ Genetics Branch

National Naval Medical Center, Bldg. 8, Rm. 5101

8901 Wisconsin Ave.

Bethesda, MD. 20889-5101

(301) 435-5436 - phone

(301) 496-0047 - fax

 

 


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