CELfiles names in a matrix
0
0
Entering edit mode
@joshi-nina-nihnci-289
Last seen 9.6 years ago
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 [[alternative HTML version deleted]]
Genetics Genetics • 681 views
ADD COMMENT

Login before adding your answer.

Traffic: 615 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6