Dear All,

I have shRNA dropout screen data obtained by using GMAP (Gene Modulation Array Platform): several cell lines, 2 time points for each, and for each cell line I would like to find the shRNAs that dropped out or at least significantly decreased across these 2 time points.

I was wondering whether limma package can be appropriate for such kind of data - just to perform differential expression analysis for each of the cell lines (with appropriate corrections for multiple testing, of course)? The data are log2-transformed intensity reads obtained from Affymetrix array (the GMAP).

Thank you very much for any help and advice!

Regards,

Anna

Matt Ritchie has used edgeR to analyze shRNA-seq screens in the past, see http://bioinf.wehi.edu.au/shRNAseq/. I suspect the same principles can be applied in your situation, with the only obvious modification required being the use of limma instead of edgeR to handle the array intensities.