I've analysed microarray data with limma package and ended up with a list of genes that are deferentially expressed. By default it has ranked DE genes based on B-statistics and from the reference manual(Page 4) I thought it would be a good parameter to rank. However from previous threads and some suggestions
adjusted p-value would be a more useful parameter to select significant DE genes. I've observed that in my results adjusted p-values are much higher (0.1 - 0.9, nothing is <0.05). what might be the reason here? Should I repeat the analysis process with any changes? Or is it normal?
And I would be interested to mention that the top DE genes selected with B-statistics are actually correlating with the experiments we are doing in the lab (The list contains the number of genes that we were assuming to have differentially expressed). I am little bit biased with this post on significance values.
- Illumina platform
- 12 completely individual cell lines (based on some experimetal results we've grouped them into 2, 6 in each)
- Normalization - neqc function from limma.
I would like to provide more information, if required.