Hello, I´m interested in finding reference genes for qPCR in my RNAseq data. I use therefore the following parameters: altHypothesis="lessAbs",lfcthreshold=0.5, alpha=0.05 to detect the most stable genes: I am not sure if I have understood this correctly: So the alternative and null hypothesis are swapped, i.e. if pval<0.05, the null hypothesis (=difference) is rejected and the alternative hypothesis (difference smaller than 0.5) is accepted.
1) Do I understand it correctly that the genes with the lowest p-value are the most stable genes when I extract my results? 2) When I ask for the summary(res), it says:
out of 67793 with nonzero total read count adjusted p-value < 0.05 LFC > 0.50 (up) : 0, 0% LFC < -0.50 (down) : 621, 0.92% outliers  : 3331, 4.9% low counts  : 61080, 90%
I´m wondering, why the summary shows the number of genes greater than my threshold, when I´m more interested in less.
3) In the Beginners guide it says: lessAbs - |β|<x - p values are the maximum of the upper and lower tests<--- what does this mean?
I`m thankful for any suggestions!