P-MTAB-33614 - P-MTAB-33614
normalisation data transformation protocol
The Tophat aligner (
) was used to align the reads to the mouse reference genome (mm9). After alignment the read counts for each gene were extracted using htseq-count (
) based on an mm9 Refseq gff file. Differential expression in our two groups was evaluated using DESeq version 1.4.1, implemented in R 2.14.1. DESeq uses a negative binomial distribution to model genic read counts following normalisation based on size factors and variance. As for the microarray analysis, p-values were adjusted by the procedure of Benjamini and Hochberg to control the type I error rate, and a cut off of p less than or equal to 0.05, and a fold change of greater than or equal to 2 were used as a threshold to define differential expression.