Open bioinfolabmu opened 8 months ago
You can add additional columns to the samples.tsv. Here is your example:
samples | stages | treatments | st |
---|---|---|---|
s1 | 4 | treatment1 | s4t1 |
s2 | 4 | treatment1 | s4t1 |
s3 | 5 | treatment1 | s5t1 |
s4 | 5 | treatment1 | s5t1 |
s5 | 6 | treatment1 | s6t1 |
s6 | 6 | treatment1 | s6t1 |
In the config.yaml, the contrast would now be: st_s5t1_s4t1
or st_s4t1_s5t1
.
Note: every sample that has a label in the contrast column will be used by DESeq2 to calculate the dispersion in your data. So it is generally best to include them all.
Question From your document, it seems that you can only use one factor to do the contrast in differential gene expression analysis. What if we need to combine two factors?
What have I tried
In my "samples.tsv", I have two different developmental stages. Each stage has three different treatments. Each treatment has 3 biological samples.
I know that I can do:
contrasts:
How about contrasts: (stages 4 treatement 1) vs (stages 5 treatment 1) or different combination of both factors?
stages | treatments
4 | Control 4 | Control 4 | Control 4 | Treatment1 4 | Treatment1 4 | Treatment1 4 | Treatment2 4 | Treatment2 4 | Treatment2 4 | Treatment3 4 | Treatment3 4 | Treatment3 5 | Control 5 | Control 5 | Control 5 | Treatment1 5 | Treatment1 5 | Treatment1 5 | Treatment2 5 | Treatment2 5 | Treatment2 5 | Treatment3 5 | Treatment3 5 | Treatment3
Thank you for your attention