Deseq2 design
1
0
Entering edit mode
Syed Zaheer ▴ 10
@ec7085d4
Last seen 10 months ago
Pakistan

Help me In deseq2 design

I have factors sex, 2species, 5stages

I want to know differential expressed genes between male and female of one species and And then from this extract I want to compare male of this species to 2nd species male

In short Regress out female effect from each stage and other species male

I designed like

Design = ~ Replicate + sex + stage + species And made ref = female

And plan to use contrast

I think something is wrong Please help how could I do this in one design I able to extract above objective for all stages

Thanks in advance

DESeq2 genes Differential expressed • 486 views
ADD COMMENT
0
Entering edit mode
ATpoint ★ 4.0k
@atpoint-13662
Last seen 2 days ago
Germany

Please show code and colData, textual descriptions are hard to follow.

ADD COMMENT
0
Entering edit mode

enter image description here gc have both sexes while tc have only male how to design this deseq2

dds <- DESeqDataSetFromMatrix(countData = Counts, colData = metadata, design = ~ Species + Sex + Stage + Replicate)

i am interested in two things DEG between male and female of Gc DEG between male of Gc and TC (for each stage as well as all combine for both comparisons)

ADD REPLY

Login before adding your answer.

Traffic: 836 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6