Question: more complicated hypotheses than differential expression (with baySeq or a similar package)
0
5.1 years ago by
United States
Will Landau0 wrote:

I have an RNA-seq dataset with 3 treatment groups, where gene g has group means mu_{g, i} for i = 1, 2, 3. Is there a way to use baySeq to calculate the posterior probabilities that mu_{g, 2} > max(mu_{g, 1}, mu_{g, 3}) and the posterior probabilities that  mu_{g, 2} < min(mu_{g, 1}, mu_{g, 3})? Specifications like groups <- list(null = c(1,1,1,1,1,1), alternative = c(1,1,2,2,1,1)) and groups <- list(null = c(1,1,1,1,1,1), alternative = c(1,1,2,2,3,3)) do not answer this question with the package's usual functionality demonstrated in the manual and the vignette. If not with baySeq, which packages can accomplish this easily?

bayseq hypotheses • 569 views
modified 5.1 years ago by Gordon Smyth39k • written 5.1 years ago by Will Landau0
Answer: more complicated hypotheses than differential expression (with baySeq or a simil
1
5.1 years ago by
Gordon Smyth39k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth39k wrote:

No, you cannot compute posterior probabilities for this hypothesis using baySeq or any other package.

People typically take a simpler approach to this sort of question. One simply conducts pairwise tests between the three groups, and then selects genes that are (i) up in group 1 relative to both groups and 3 or (ii) down in group 1 relative to both groups 2 and 3. This sort of analysis is done every day using any of the RNA-seq analysis packages such as edgeR, limma, DESeq, baySeq.