[BioC] edgeR for paired-end and strand specific data

[wang peter]

I am using edgeR to analyze my RNA-seq data
the data is paired-end and strand specific

i have 6 sample
1-3 are biological replicate of one tissue
4-6 are biological replicate of the other tissue

the problem is for one sample, there are two values, forward
expression value and reverse expression value,
although most of reverse expression value are zero, due to strand
specific experiments
but i cannot use only forward expression value for one sample.

if i want to keep both forward expression value and reverse expression
value, how can i design
the model.matrix, thx
-- 
shan gao
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Boyce Thompson Institute
Cornell University
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