Transcriptomic data analysis

Question

[asmita.bt14]

Hi,

Hope everyone is doing good. I am doing transcripyomic data analysis of control vs transgenic to find the difference in expression their pattern but as I started my study I found that FPKM value of internal control genes are higher than transgenics. I would really appretiate your help if anyone can guide how to normalize the data and then do analysis?

Answer 1

[i.sudbery]

You can't do transcriptomics data analysis by comparing FPKM values of genes between samples. Transcriptomic data require careful normalisation and specialised statistical tests. Any one of a number of packages are available to perform differential analysis of transcriptomic data.

Please see vignettes for the following popular R packages:
DESeq2
EdgeR
Limma/Voom