How to find that genes are up or down-regulated in which condition

Question

[StartR]

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

head(lm$coefficients)
         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

Answer 1

[ATpoint]

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

[StartR]

Thank you, that's very helpful :)