Deseq2 shows differential expression while TPM values are not significantly different

Question

[Aiswarya]

Hi,

I am trying to find difference in expression of a gene. I find that the gene is differentially expressed between my condition when I perform deseq2, however it shows no statistically significant difference, when expression is compared as TPMs, using a t-test.

Is there an explanation for this?

Thanks in advance!

[jv]

There is no recommendation for using TPM values to compare gene expression between samples. One of the reasons DESeq was developed was because most RNA-seq experiments are underpowered for conventional statistical tests like the t-test

[ATpoint]

If tests and normalization methods were perfectly the same they would not coexist. For a more elaborate answer you need to add code or plots.