Deseq2 design
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Syed Zaheer ▴ 10
@ec7085d4
Last seen 18 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 • 681 views
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ATpoint ★ 4.6k
@atpoint-13662
Last seen 56 minutes ago
Germany

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

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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)

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