Question: Rank Products- breast cancer
0
gravatar for Eleni Christodoulou
11.0 years ago by
Singapore
Eleni Christodoulou150 wrote:
Dear list, I would like to apply the Rank Products method in a two-color experiment on breast cancer data in order to identify differentially expressed genes between ER+ and ER- samples. I downloaded the R-package RankProd and tried to use the RP function. The experiments were done with a common reference for all the samples examined. So the sample of interest was at the one channel and the reference on the other. I was wondering in the RP function: RP(data,cl,num.perm=100,logged=TRUE,na.rm=FALSE,gene.names=NULL,plot=F ALSE, rand=NULL), where cl is said to be: cl: a vector containing the class labels of the samples. In the two class unpaired case, the label of a sample is either 0 (e.g., control group) or 1 (e.g., case group). For one class data, the label for each sample should be 1. Can I use 1 for ER- and 0 for ER+ samples from the matrix that I have? My matrix contains gene expressions as rows and samples as columns. The columns are only the samples of interest (ER+, ER-), not the reference. I am a bit confused with the exact meaning of "control group" and "case group". Thanks a lot! Eleni [[alternative HTML version deleted]]
cancer rankprod • 477 views
ADD COMMENTlink written 11.0 years ago by Eleni Christodoulou150
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 320 users visited in the last hour