Created
March 11, 2013 19:37
-
-
Save sashaphanes/5137016 to your computer and use it in GitHub Desktop.
same as RPKM.R
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| >dataFile = "fileOfInterest.txt.gz" | |
| >rawdata = read.delim(gzfile(dataFile), sep="\t", header=T) | |
| >rownames(rawdata) = paste(rawdata[,"Chr"], rawdata[,"GeneSym"], sep = ".") | |
| >data.RPKM = rawdata[, grep("RPKM", colnames(rawdata))] | |
| >rowMax = do.call("pmax", c(data.RPKM[,1:ncol(data.RPKM)],na.rm=TRUE)) | |
| >data.RPKM.rowMax.gt1 = data.RPKM[rowMax >1,] | |
| >data.RPKM.rowMax.gt1[is.na(data.RPKM.rowMax.gt1)] = 0 | |
| >data.RPKM.log2 = log2(data.RPKM.rowMax.gt1 + 1) | |
| >RNAseq.RPKM.log.m = as.matrix(data.RPKM.log2) | |
| >library(limma) | |
| >library(affy) | |
| >RNAseq.RPKM.log.m.qNorm = normalizeBetweenArrays(RNAseq.RPKM.log.m, method="quantile") |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment