I am looking at an experiment with 5 comparisons (and not much difference among the conditions). I tried separating out one comparison from all the system, running DESeq2 on it separately. This resulted in lowering the lfcSE for some genes, making more genes significant.
1) Are there any indications for discerning whether these additional significant genes are real or false positives?
2) I looked at the normalized counts for the analysis which includes all conditions, as well as the one where there is only one comparison. The expression values are very similar. What can explain the difference in lfcSE?
The analysis with the compared two conditions (treatment & control) only
Control1 Control2 Control3 Control4 Treat1 Treat2 71461.7 81214.1 89435.5 69952.7 122438.9 115726.5 baseMean log2FoldChange lfcSE stat pvalue padj 91704.9 0.622783439312684 0.103093524641065 6.04095593279012 1.532038E-09 1.01581793E-05
For the analysis with all conditions ( there are other conditions besides treat & control, but I omit them here):
Control1 Control2 Control3 Control4 Treat1 Treat2 65019.9 74355.1 85325.1 67412.9 112764.2 110093.7 baseMean log2FoldChange lfcSE stat pvalue padj 84231.6928842715 0.621226842710026 0.313839691139753 1.97944001427593 0.047766487091329 0.998357130543871
The values of the samples are not very different, yet there is a large difference in the stat and pvalue (based on a difference in lfcSE). What could be the cause for that?
3) What is the lfcSE dependent upon, generally speaking? I admit that the 2014 is above my level in statistics.