Thanks Lorena and Steve. Using the DeSeq2 I was able to get a list of genes after FDR adjustment. We do some expected functional enrichment there which is great. I would be curious to know the changes in DESeq2 but I guess the paper is not yet out. Cheers! -Abhi On Tue, Oct 15, 2013 at 1:33 PM, Lorena Pantano wrote: > Hi, > > this could happen if your model doesn't explain all your design. There is > good example in the tutorial about plotting pvalues to see if you get the > expected distribution. > > Sometime I get the same, and in some cases, although FDR is not so low, if > I do a heatmap of the top genes, I get my data clustered into the groups I > have in my model (cases versus control for instance). So, sometimes there > is signal even if FDR is higher than 0.1. But you need to be very careful > and really look your data using other visual representation as others have > suggested. > > cheers > > > > > Lo > > > On Tue, Oct 15, 2013 at 7:50 PM, Abhishek Pratap wrote: > >> Hi Everyone >> >> Given the study design( see below) I am somewhat surprised NOT to see any >> genes being differentially expressed with p.adj < .05 or .10. I would like >> the help from folks on this mailing list to introspect the analysis and >> figure out if we overlooked something or data >> >> >> Study Design: >> 4 cases v/s 4 control ( all replicates are biological) >> One sample in the case had very low read counts but I thought that should >> not make a lot of difference in case of DESeq. I did however try to re-run >> the analysis taking that out but no change as far as the #diff exp genes. >> >> Analysis done with : DESeq_1.12.0 >> >> > sizeFactors(cds)TRA00010811 TRA00010812 TRA00010816 TRA00010813 >> TRA00010814 TRA00010817 TRA00010818 >> >> 0.9834455 1.3122005 0.7464998 1.3739400 1.6820479 >> 0.5693563 0.7763204 >> >> >> >> metadata >> >> >> condition libType >> TRA00010811 ablated paired-end >> TRA00010812 ablated paired-end >> TRA00010816 control paired-end >> TRA00010813 ablated paired-end >> TRA00010814 ablated paired-end >> TRA00010817 control paired-end >> TRA00010818 control paired-end >> >> >> >> Attached: >> dispersion plot and MA plot >> >> Please let me know if you need anything more from my end to help me dig a >> bit deeper and understand what might be going on here. >> >> Thanks a lot, >> -Abhi >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]