Question: Differential expression analysis of transcriptome data
gravatar for vijay
4.0 years ago by
vijay1.5k wrote:

Dear Folks,

I am currently working on brain transcriptome data of a male and female fish obtained using RNASeq. I wish to compare them and obtain the differentially expressed genes. All that I have got is a table containing the Transcripts per milllion (TPM) and the FPKM value for both the samples. I went through a few references which suggested to take log(fpkm) as the differential expression measure. However, I am interested in determining the statistical significance and determine the p-value and FDR of the differentially expressed genes. I learnt that few R packages like DESeq and EdgeR can do this job for me. Unfortunately, I am stuck up in using them as I understand that the TPM or FPKM values are not usable in those packages. Please can someone help me in sorting out this issue and let me know what is required to be done?

I am very much novice in this field and this is my first hands on with RNAseq data. Any help would be greatly appreciated.


transcriptome rna-seq deseq • 1.7k views
ADD COMMENTlink modified 4.0 years ago by Thibault D.670 • written 4.0 years ago by vijay1.5k

Hello Chennai

Did you resolve your problem?. I have a similar doubt. I have the list of fpkm of genes and I want use R packages

ADD REPLYlink written 3.3 years ago by vm.higareda20
gravatar for Thibault D.
4.0 years ago by
Thibault D.670
European Union
Thibault D.670 wrote:


Packages such as DESeq2, uses their own normalisation methods. You should give them raw counts (the original and non-normalizes ones). You can run tools such as htseq-count or feature-count on your bam files to get your raw counts.

Have a look at the section 1.3.1 of the DESeq2 manual to understand :)

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Thibault D.670

Thanks for your response. Please can you let me know if explaining differential expression only based on log(FPKM) values will make sense. In other words, is that technically correct and acceptable for publication?

ADD REPLYlink written 4.0 years ago by vijay1.5k


It isn't. Shortly, FPKM is a within-sample normalized expression metric and shouldn't be compared between samples.

ADD REPLYlink written 4.0 years ago by Carlo Yague4.8k
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