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bioinfo-biols / CIRI-cookbook

Document for CIRI-series software
https://ciri-cookbook.readthedocs.io/en/latest/index.html
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A question about the results of differential expression analysis #27

Open abedkurdi opened 1 year ago

abedkurdi commented 1 year ago

Hello everyone,

I downloaded 5 TCGA-BRCA samples (by choosing specific criteria - I got five tumor samples and their five normal samples) and I run CIRIquant on them. I performed differential expression analysis using CIRI_DE_replicate and I got the final table. My question is: Do you have any idea why would I get good log2 fold change values but not statistically significant (all FDR values are greater than 0.05)?

I appreciate your advice and thanks in advance.

abedkurdi commented 1 year ago

It seems TCGA RNA-seq data are not total RNA-seq data. They are mRNA-seq. Maybe this is why I am getting insignificant results.