Hi, I'm relatively new to bioinformatics, and have been following the Galaxy pipleine for my RNA seq data. At this stage, I have featureCounts count tables.
In one one of the DEG experiments, I have to compare WT baseline data (2 males + 2 females) vs WT at 1h (2 males + 2 females). I am using "Timepoint" as my primary Factor, and the 2 groups mentioned before as my Factor Level 1 and 2 respectively. Thus, my primary comparison will be between these groups. However, to control for the variance in sex, from browsing Galaxy tutorials and info pages, I was drawn to the conclusion that I can introduce "Sex" as a secondary factor, and contrast 'Males' - Factor Level 1 with 'Females' - Factor Level 2. This seems a bit counter-intuitive to me, so I would really appreciate some advice on how to introduce sex as a variable in Galaxy DESeq2.
These are some examples I saw on Galaxy that pertain to this issue:
-> under "Inputs" in the DESeq2 tool on Galaxy
"The following table gives some examples of factors and their levels:
Factor Factor level 1 Factor level 2
Treatment Treated Untreated
Condition Knockdown Wildtype
TimePoint Day4 Day1
SeqType SingleEnd PairedEnd
Gender Female Male
Note: Output log2 fold changes are based on primary factor level 1 vs. factor level2. Here the order of factor levels is important."
&
-> under "Hands-on: Determine differentially expressed features"
Thanks in advance!
István