A question concerning the interpretation of microarray expression data -
After running GEO2R, which uses limma-based package for value comparison, I got a table of genes with their
"ID" "adj.P.Val" "P.Value" "t" "B" "logFC" "Gene.symbol" "Gene.title"
From what I read on google, B-value and the moderated t (and hence P or adj P value) should rank the genes in the same order, which is true for my output table. However, according to other postings on google, only probes with positive B-values are thought to have a "differential expression". In my output, among the 54000 probes, only 85 probes show a "SIGNIFICANT" p-value (<0.05) but with positive B-values (many with p-value <0.0006 also have negative B-values).
How do we interpret those probes with low p-value but negative B-values ? Any suggestion or direction for more information on this issue ? Great many thanks.