Hi everyone.
I performed RNA-seq experiment on two independent groups for Group1 and Group2. number of Group1 samples is 15 and number of Group2 samples is 4. and number of genes is 20000.
And I am doing rna-seq data analysis using mt.maxT function of multtest R package (Permutation 5000).
this is summary data
summary(PP$index)
Min. 1st Qu. Median Mean 3rd Qu. Max.
1 5126 10251 10251 15376 20501
summary(PP$teststat)
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-5.5036 -1.1150 -0.0513 -0.0511 0.9765 8.0654 878
summary(PP$rawp)
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0004 0.1404 0.3884 0.4334 0.6998 1.0000 878
summary(PP$adjp)
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0580 1.0000 1.0000 0.9992 1.0000 1.0000 878
summary(PP$fdr)
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.2102 0.5610 0.7761 0.7387 0.9330 1.0000 878
my smallest fdr p-value among 20000 genes is 0.21 and unadjusted p-value among 20000 genes is 0.0004.
In this situation, can I set cutoff using raw p value (unadjusted p value)?
Thanks h.mon.
I can't use other tools (edgeR or DESeq2). Because My data is quartile normalized by TCGA pipeline (no TCGA data). Additionally, I have only rsem quartile normalized data. :(