How to find that genes are up or down-regulated in which condition
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Entering edit mode
16 months ago
StartR ▴ 20

Hi,

I have a very fundamental question,

If we are doing differential gene expression analysis - for example - Between condition 1 vs Condition 2 via either Limma, DESeq or edgeR,

How to find out that the results that we got - up and down-regulated gene list - are deferentially expressed in Condition 1 vs 2 or they are differentially expressed in Condition 2 vs 1? meaning are they up or downregulated in Condition 1 as compared to condition 2 or they are up and down regulated in condition 1 as compared to condition 2?

I have done something like this in Limma:

design_matrix <- model.matrix(~0+matrix_model)

colnames(design_matrix) <- c('Low', 'High')

$contrasts Contrasts Levels High - Low Low -1 High 1$design
Low High
1   1    0
2   0    1
3   1    0
4   1    0
5   1    0

Contrasts
High - Low
A1BG    -0.2442607336
A1CF    -0.0004826392
A2M      0.4969213243
A2ML1    0.1609067551
A3GALT2  0.0154397887
A4GALT   0.0761423508


So - here - my conditions are - Low and High

How to find that the resulted gene list are up/down-regulated in High as compared to low or they up/down-regulated in Low as compared to High?

Looking forward to a valuable answer

Thanks

enrichment sequencing python genomics • 617 views
2
Entering edit mode
16 months ago
ATpoint 64k

The contrasts indicate that High (1) is the counter and Low (-1) the denominator so a positive fold change means upregulated in High.

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Entering edit mode

Thank you, that's very helpful :)