Question: DGE with PEER normalized data
gravatar for Prasad
3.2 years ago by
Prasad1.6k wrote:

I am working with time series RNA-seq data(10 samples, each with 3 biological replicates). I performed sample clustering using hclust but the replicate wise clusters were not proper, so I was asked to do further normalization of FPKM values using PEER R package . Now I want to calculate differential expression using this normalized data but could not find any appropriate packages. This is how my normalized data looks like.

Transcript_ID   A   B   C
Contig10    6.50308322747151E-007   -3.90183130249966E-009  2.78059042457812E-009
Contig9999  7.53524395658012E-011   8.57470422488404E-006   -1.14360755105736E-005
Contig9995  0.000002363 0.0001350445    -4.99606248922646E-005

As per the suggestions I am trying out voom in limma not so sure about it so please suggest some packages which can take normalized data for getting DEG's.

dge rna-seq R • 934 views
ADD COMMENTlink modified 3.1 years ago • written 3.2 years ago by Prasad1.6k
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