[BioC] using easyRNASeq to calculate RPKM values
Fatemehsadat Seyednasrollah
fatsey at utu.fi
Tue Jan 22 14:03:19 CET 2013
Dear list,
I have used HTSeq to get the count table of an RNA seq dataset which has 8 biological replicates and two conditions ( so 4 biological replicates for each condition ) and the count table is like below:
> head(a)
V1 V2 V3 V4 V5 V6 V7 V8 V9
1 1/2-SBSRNA4 3 5 4 4 2 3 1 1
2 A1BG 200 93 246 102 86 46 58 85
3 A1BG-AS1 24 28 16 32 17 10 19 14
4 A1CF 1 1 1 2 1 0 0 1
5 A2LD1 100 71 98 97 59 128 88 114
6 A2M 5 5 23 1 5 6 10 5
Now for getting familiar with the expression level of each gene I want to calculate the RPKM values. Can I use the easyRNASeq package over the above count table to calculate the values or not?
Thank you in advance
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