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.