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Monthly Archives: January 2011
Perl and SAM
Lincoln Stein has written a bunch of modules to deal with SAM/BAM files. Check out the CPAN module. To install the Perl module on a machine where you don’t have root access, follow these instructions. Using this module, I recreated … Continue reading
Normalisation methods for DGE data
So I created a dataset with 4 samples; column 1 and 2 are the controls and column 3 and 4 are the patients. 25 transcripts are in all 4 samples in equal amount. Another 25 transcripts are only in the … Continue reading
DESeq vs. edgeR vs. baySeq
6th April 2012: For a more updated version of this post, please refer see this post. A very simple comparison Using the TagSeqExample.tab file from the DESeq package as the benchmark dataset. According to DESeq authors, T1a and T1b are … Continue reading
DESeq
Code taken from the DESeq vignette for my own convenience. library(“DESeq”) exampleFile = system.file (“extra/TagSeqExample.tab”,package=”DESeq”) countsTable = read.delim(exampleFile, header=TRUE, stringsAsFactors=TRUE) rownames(countsTable) = countsTable$gene countsTable = countsTable[ , -1] conds = c(“T”,”T”,”T”,”Tb”,”N”,”N”) cds = newCountDataSet (countsTable, conds) cds = cds[,-1] cds … Continue reading