Question: differential gene expression based on transcript abundance
0
gravatar for cloverchicken
3.3 years ago by
cloverchicken0 wrote:

Hello there,

I am a newbie to transcriptomic analysis, so it would be grateful if anyone can help me out these issues.

I got a table of transcript abundance from a company has done transcriptomic analysis. First, I try with Deseq but an error came up, and it said my data is not integer so I can't proceed further. Then I tried to round up my data and it worked, but it seems like I lost quite a lot transcript information.

Second, I have 4 treatments, and 3 biological replicates per each treatment, in total, I have 12 samples. As following Deseq protocol, it uses nbinomTest (compare only 2 treatments), which test should I use for 4 treatments? I also tried with 2 treatments of my data, and the heat map still showed 4 treatments (12 columns) but not in order.

Third, how do I call the candidate genes from my data?

Does anyone have any idea about these issues?

Thank you and have a good day.

rna-seq R • 917 views
ADD COMMENTlink written 3.3 years ago by cloverchicken0

Try to be more informative when asking questions. How was the transcript abundance data generated? Do you have access to the original data?

I suspect kallisto or salmon was used and would suggest tximport workflow, but that's just a guess based on limited information.

ADD REPLYlink written 3.3 years ago by WouterDeCoster43k
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