Hi all, i am using NOISeq with biological replicates.(i saw the Warning: NOISeq for biological replicates has not been tested yet. In case you use it, we will be very grateful to receive any feedback from you! , so, it will be a feedback in the end..) I have 2 conditions with 3 replicates for each. I normalized my data by using "tmm". i execute NOISeq as: myresults <- noiseq(mytmmdata_a,mytmmdata_na,repl = "bio" , k=0.5 , norm="tmm" , long=1000, q=0.8, nss=0) My question is on the "q" parameter. Usually significant is when p.v = 0.05. What "q" value equal for that? What is the "q" test? how calculate? Thanks, Papori -- output of sessionInfo(): R version 2.14.0 (2011-10-31) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] edgeR_2.4.3 limma_3.10.3 loaded via a namespace (and not attached): [1] annotate_1.32.2 AnnotationDbi_1.16.19 Biobase_2.14.0 DBI_0.2-5 DESeq_1.6.1 [6] genefilter_1.36.0 geneplotter_1.32.1 grid_2.14.0 IRanges_1.12.6 RColorBrewer_1.0-5 [11] RSQLite_0.11.1 splines_2.14.0 survival_2.36-12 tools_2.14.0 xtable_1.7-0 -- Sent via the guest posting facility at bioconductor.org.