q-value or local FDR
Hello all,
I have some RNA-SEQ data and do some analysis by metaseq package for meta-analysis,for choosing genes I calculate q-value and local FDR,but after using local FDR<0.1 for upper and lower of fisher and stouffer, I don't have any genes for S$Lower and F$Lower,because value of local FDR for all of my analysis are 1 or .99, so it means that every time I do not have down-regulate genes in every analysis!while I have genes for S$Upper and F$Upper.
Besides, for threshold q-value<0.1,I have some genes not only up-regulated DEGs but also down-regulated DEGs.
can I use q-value?and what is difference between q-value and local FDR in term of statistical accuracy?
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Can you describe more in detail what you are doing?
by metaseq package,in the end p-value is calculated as "two-sided" test,for finding DEG I want to use fdr,so I use q-value package,by this package we have q-value and local FDR,as I said after using local FDR<0.1 I don't have down-regulate genes but threshold q-value<0.1,I have some genes
And how does your data look like, why do you use a meta analysis?