Question for the results of singlecell::MAST

[yecotoo]

Hello! There is a problem and I don't know why. I used Singlecell::NAST to find the DEGs between group A and B and found something curious and confused. How the avg_logFC of gene CD34 is > 0 (cause A.pct < B.pct and A.exp < B.exp)? I'm sure I have set the group B as the control. some gene show the right trend such as 1110004E09Rik. I wonder what makes it happen? Is the code wrong. Please help me. Thanks!

gene	avg_logFC	A.pct	B.pct	A.exp	B.exp
CD34	0.016416362	0.281	0.407	0.38410596	0.544973545
--	--	--	--	--
1110004E09Rik	-0.612574252	0.04	0.063	0.043046358	0.063492063
--	--	--	--	--	--

[AlanTeoYueYang]

We are using Seurat logFC to calculate it. We pushed a recent update where you can set the factor to the label column. This ensures that label1 is the reference point.

[yecotoo]

OK！thanks, have a nice day ---- Replied Message ---- ***@***.***>Date3/15/2025 ***@***.***>***@***.***>, ***@***.***>SubjectRe: [neurorestore/Libra] Question for the results of singlecell::MAST (Issue #63) We are using Seurat logFC to calculate it. We pushed a recent update where you can set the factor to the label column. This ensures that label1 is the reference point. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***> AlanTeoYueYang left a comment (neurorestore/Libra#63) We are using Seurat logFC to calculate it. We pushed a recent update where you can set the factor to the label column. This ensures that label1 is the reference point. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>