Deseq2 shows differential expression while TPM values are not significantly different
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!
• 1,117 views
•
link
updated
by
jv
•
written
by
Aiswarya •
•
written
by
Aiswarya •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Discrepancy in GEO2R vs. Raw Data Analysis: Significance of DEGs
written by Saeedeh Salehi •
-
Using Pseudobulk Approach for Identifying Marker Genes Within a Single Condition
written by nhaus •
-
How to properly use DESeq2 for an experiment
written by Aurélien •
-
Quality Check of Samples and Biological Replicates
written by doinelpierrot •
-
Finding biomarkers between tumor and normal samples
written by glady
-
Unequal sample sizes Deseq2
written by Payal
-
Differential analysis show different results with edgeR and in box plot with t-test
written by newbie
-
edgeR again: can you AND multiple conditions for analysis?
written by moxu
-
Comparing two differential expression experiments
written by user31888
-
Comparing lists of differentially expressed genes
written by ra381 •
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.
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