Question: DEG analysis grouping help
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gravatar for sir.outman
7 days ago by
sir.outman0
sir.outman0 wrote:

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):

  1. cancer cells with nothing added;
  2. cancer cells with tgfb only;
  3. cancer cell with tgfb and compound a;
  4. cancer cell with tgfb and compound b;
  5. cancer cell with tgfb and compound c, (compounds a,b,c are inhibitors of tgfb);

My questions are:

  1. How do I set up group information for DEGs ?
  2. 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?

  1. 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.

rna-seq deseq2 • 76 views
ADD COMMENTlink written 7 days ago by sir.outman0

Cross-posted here: https://bioinformatics.stackexchange.com/questions/14889/deg-analysis-grouping-help

Instead of cross-posting, would you mind adding more information? What is unclear, the DESeq2 manual gives detailed instructions on the standard analysis pipeline? Where do you get stuck? Try to be precise.

ADD REPLYlink written 7 days ago by ATpoint42k
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