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differential gene expression based on transcript abundance

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
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written by cloverchicken • cloverchicken

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.

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written by WouterDeCoster WouterDeCoster

I think DESeq uses read counts which are never decimals so you shouldn't have to round up

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written by peter.brockport • peter.brockport

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