Perl and SAM

Lincoln Stein has written a bunch of modules to deal with SAM/BAM files. Check out the CPAN module. If you are having trouble installing Bio::DB::Sam, you may have to recompile SAMTools with the following command: To install the Perl module on a machine where you don't have root access, follow these instructions. Using this module,...

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Normalisation methods implemented in edgeR

Updated 2014 December 12th A short post on the different normalisation methods implemented within edgeR; to see the normalisation methods type: From the documentation: method="TMM" is the weighted trimmed mean of M-values (to the reference) proposed by Robinson and Oshlack (2010), where the weights are from the delta method on Binomial data. If refColumn is...

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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 similar, so I removed the second column in the file corresponding to T1a: Hierarchical clustering...

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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 = estimateSizeFactors(cds) sizeFactors(cds) cds <- estimateVarianceFunctions( cds ) res <- nbinomTest( cds, "N", "T" )...

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