[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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