Hi, I am processing a set of around 40 Affymetrix hybridizations of (I think) quit good quality. When I run limma on the rma-normalized set, everything runs smoothly. > fit<-lmFit(eset.rma, design) > fit<-eBayes(fit) However when I do the same thing on the gcrma-normalized set, I receive a warning: > fit<-lmFit(eset.gcrma, design) > fit<-eBayes(fit) Warning message: In ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim) : Estimation of var.prior failed - set to default value Could somebody explain me, what this possibly means and if this might affect the results in any adverse way? Any help will be appreciated. Best, Georg > sessionInfo() R version 2.7.1 (2008-06-23) x86_64-redhat-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] affycoretools_1.12.0 annaffy_1.12.1 KEGG.db_2.2.0 [4] gcrma_2.12.1 matchprobes_1.12.0 biomaRt_1.14.0 [7] RCurl_0.9-3 GOstats_2.7.0 Category_2.6.0 [10] genefilter_1.20.0 survival_2.34-1 RBGL_1.16.0 [13] annotate_1.18.0 xtable_1.5-2 GO.db_2.2.2 [16] AnnotationDbi_1.3.8 RSQLite_0.6-9 DBI_0.2-4 [19] graph_1.18.1 affy_1.18.2 preprocessCore_1.2.0 [22] affyio_1.8.0 Biobase_2.0.1 limma_2.14.5 loaded via a namespace (and not attached): [1] cluster_1.11.11 XML_1.95-2