[BioC] CELfiles names in a matrix

James MacDonald jmacdon at med.umich.edu
Thu Apr 1 00:01:38 CEST 2004

sampleNames is not a variable that can be passed to justRMA (see
?justRMA for the help file). If you want the column names to be the cel
file names, just do

Data1 <- justRMA ( phenoData=pD1)

You will have to hand enter 'Gene Names' in the first cell of the
spreadsheet. You could probably hack the code for read.table() to get it
to put 'Gene Names' in the spreadsheet automatically, but I doubt it
would be worth the effort.


James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> "Joshi, Nina (NIH/NCI)" <joshini at mail.nih.gov> 03/31/04 03:38PM
I am uploading cel files with the command justRMA.  I create a
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
number and/or names in rows.  The output file appears to have the
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
files listed in columns (133 cases) and the correct number of genes
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







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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