Hi.

I’ve a question regarding lfcShrink coef option. I've read that it is better to use the option “coef” rather than “contrast”.  However, I have a case where the resultsNames(dds) does not contain the desired contrast coefficient.

For example (the names of the groups have changed for clarity. This can result in different coefficients list):

> table(colData(dds)$group)

A B C D E F G
3 2 3 3 3 4 3

> resultsNames(dds)
[1] "Intercept"                                     "group_B_vs_A" "group_C_vs_A"
[4] "group_D_vs_A"    "group_E_vs_A"    "group_F_vs_A"    
[7] "group_G_vs_A"

The coefficient in which I was interested to “shrink” was group_F_vs_G

What should be done in that case? Should the “contrast” option be used instead or a linear combination of coefficient?

Thanks in advance.

Victor.

hi Victor,

Yes, you should use 'contrast'. We will continue to support the use of 'contrast' in lfcShrink(), which will give LFCs as described in the DESeq2 paper.