Deseq2 shows differential expression while TPM values are not significantly different
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7 weeks ago
Aiswarya ▴ 10

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!

Deseq2 TPM • 297 views
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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

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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.

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