Hi all,

My question concerns testing interactions using the group design and the use of lfcShrink():

As a short intro, my experimental design:

- three treatments: control, mild, severe
- three developmental zones: mer, elo, mat

Before lfcShrink() was introduced, the resultsNames() function would produce all groups formed and you could simply use the contrast function to compare groups:

> resultsNames(dds_withint_forgroupanalysis)
 [1] "Intercept"       "groupcontrolelo" "groupcontrolmat" "groupcontrolmer" "groupmildelo"    "groupmildmat"    "groupmildmer"   
 [8] "groupsevereelo"  "groupseveremat"  "groupseveremer" 

results(dds_withint_forgroupanalysis2, contrast=c("group", "mildelo", "controlelo"))

Now, the same analysis does not yield these groups anymore but comparisons with "_vs_" (DESeq2 v1.18):

> resultsNames(dds_withint_forgroupanalysis2)
[1] "Intercept"                      "group_controlmat_vs_controlelo" "group_controlmer_vs_controlelo" "group_mildelo_vs_controlelo"   
[5] "group_mildmat_vs_controlelo"    "group_mildmer_vs_controlelo"    "group_severeelo_vs_controlelo"  "group_severemat_vs_controlelo" 
[9] "group_severemer_vs_controlelo"

(Q1) Can you still use the results produced by the contrast functionality with the group names, e.g. controlmat, mildmer, ... (even though the names produced by the resultsNames()-function are different, e.g. group_mildmer_vs_controlelo)? Because it still produces LFCs, pvalues, ... For example:

results(dds_withint_forgroupanalysis2, contrast=c("group", "mildelo", "controlelo"))

Concerning lfcShrink(): In another post (https://support.bioconductor.org/p/98833/#98837), it is advised to work with coef instead of contrast. Here I understand that you can use each coef present in the resultsNames() output. Yet there are only 9 contrasts shown (many more are possible) and some of the contrasts which I want to use are not represented, for example: group_severemat_vs_controlmat.

(Q2) How can I overcome this and use the coef for all possible contrasts? Now I have to do contrasts where I compare all the groups (related to my first question), yet using contrasts and coefs generate different LFCs (as explained in: https://support.bioconductor.org/p/98833/#98837)

For example:

lfcShrink(dds_withint_forgroupanalysis2, coef = 7)
lfcShrink(dds_withint_forgroupanalysis2, contrast=c("group", "severeelo", "controlelo"))

Thank you in advance!

Kind regards,

Jonas

DESeq2 version: 1.18.1, R-version 3.4.4.

Q1: Yes, results() takes care of this for you. Q2: ‘coef’ is only slightly preferred in that our latest greatest estimator is built around it, but you can continue to use ‘contrast’ with type=“normal” or “ashr”.