On identifying differentially expressed genes using RNA-Seq (fpkm) data.

Question

[Eric Wang]

I just have FPKM RNA-seq gene expression data, I would like to ask which software or R-package can use fpkm data to identify differentially expressed genes.

[lakhujanivijay]

Can you tell us how the FPKM was calculated?

• if somebody calculated for you, can you provide us the details of software/program?
• or did you write your own program.
• or did you used already available program/package?
• or if you downloaded the data from somewhere, if yes, which source?

[Eric Wang]

I downloaded the FPKM data from GEO database. They just provided the FPKM data matrix. For raw count data, they provided SRA format sequencing data. However, I am in urgent need of data analysis, so I would like to ask if there is any differentially expressed gene analysis method for FPKM.

[Benn]

No there are not sound methods to do DE analysis with FPKM values. To do sound statistics use counts, and then use limma voom or edgeR or the like. If you still want to use FPKM values, feel free to do it, but don't ask for the best method, because there ain't one.

[Eric Wang]

Thank you for your help! I will try to obtain DE genes using raw counts.