Question: more complicated hypotheses than differential expression (with baySeq or a similar package)
0
gravatar for Will Landau
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
ADD COMMENTlink 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
gravatar for Gordon Smyth
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.

ADD COMMENTlink written 5.1 years ago by Gordon Smyth39k

Thanks, that sounds reasonable. 

ADD REPLYlink written 5.1 years ago by Will Landau0
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