Hi everyone: I'm new to rna_seq data analysis. I'm going to analyze mRNA sequencing data from a certain cancer cell and drug treatment for DEGs using DESeq2.
The samples are prepared and sequenced as follows(every sample have two repeats):
- cancer cells with nothing added;
- cancer cells with tgfb only;
- cancer cell with tgfb and compound a;
- cancer cell with tgfb and compound b;
- cancer cell with tgfb and compound c, (compounds a,b,c are inhibitors of tgfb);
My questions are:
- How do I set up group information for DEGs ?
- I planned the following combination:
- tgfb+empty cell;
- tgfb+compounds a,b,c;
- empty+compounds a,b,c;
after this grouping, three analyses were performed to obtain the differential genes between the three combinations. Are these groups correct?
- If empty cell is used as a control and grouped as four groups for one single analysis like: empty cell , tgfb, tgfb+a, tgfb+b, tgfb+c, does this make sense and how can the DEGs obtained be explained?
I am very confused, please help me.