Entering edit mode
Hi,
I have a quick question regarding how to use lfcshrink when I want to compare the expression of one group (B) to two other groups together (C+D).
This is what I ran tried to compare group A with the combination of group B and C with design = ~0+ Condition, but when I tried to use listValues with lfcShrink it didn't work.
resultsNames(dds) [1] "ConditionA" "ConditionB" "ConditionC" "ConditionD" [5] "ConditionE"
NR <- results(dds, contrast=list(c("ConditionB"),c("ConditionC","ConditionD")),listValues=c(1, -1/2))
I found out from a post that lfcShrink does not support list values, but then how can I perform shrinkage if I had to use list values in my contrast? Any suggestions will be appreciated!
Hi Michael,
Thank you for your quick reply! Just to confirm that I understand this correctly, would this be the right contrast to use in my case?
Hmm, check
resultsNames(dds)... that doesn't seem to match what you wanted to do in your original post.Hi Michael,
Thank you for your reply, but I am a little bit confused about what you said. What I meant in my original post was how to perform shrinkage using lfcShrink on a comparison between group B and group (C+D), which from reading previous posts requires using listValues in contrast.
This is what my resultNames(dds) looks like:
I went back to read more on using numeric contrast and based on this documentation section 3.2, my understanding is that if I want to compare Condition B with (Condition C + Condition D), it would be Condition B - 0.5(Condition C + Condition D).
Corresponding to the resultNames(dds): "ConditionA" "ConditionB" "ConditionC" "ConditionD" "ConditionE" 0 1 -1/2 -1/2 0
Is this an incorrect understanding of the use of numeric contrast?
Sincerely
Oh I was reading the part “group A with the combination of group B and C”.
Your code looks fine then for the other comparison.
Very sorry for the confusion and thank you!!!