[BioC] Interspecies differential expression of orthologs with Edger

[assaf www]

Dear Gordon thanks,

Suppose I start with the following matrices:

# 'counts' is the Rsem filtered counts
> counts[1:4,]
                     h0  h1  h2  n0  n1  n2
ENSRNOG00000000021   36  17  20  10  25  38
ENSRNOG00000000024 1283 615 731 644 807 991
ENSRNOG00000000028   26  12  11  18  23  28
ENSRNOG00000000029   22  13  12  16  17  15

# 'geneLength' is the species-specific gene lengths, for species 'h' and
'n':
> geneLength[1:3,]
                   h0.length h1.length h2.length n0.length n1.length
n2.length
ENSRNOG00000000021      1200      1200      1200      1303      1303
1303
ENSRNOG00000000024      1050      1050      1050      3080      3080
3080
ENSRNOG00000000028      1047      1047      1047      1121      1121
1121


does the following code look correct, and may allow allows across species
analysis ?:
(technically it works, I checked)

# quantile normalization: (as in here:
http://davetang.org/wiki/tiki-index.php?page=Analysing+digital+gene+expression
)

x1 = counts*1000/geneLength
library(limma)
x2 = normalizeBetweenArrays(data.matrix(x1),method="quantile")
offset = log(counts+0.1)-log(x2+0.1)

...

y <- estimateGLMCommonDisp(y,design,offset=offset)
y <- estimateGLMTrendedDisp(y,design,offset=offset)
y <- estimateGLMTagwiseDisp(y,design,offset=offset)
fit <- glmFit(y,design,offset=offset)

...


Thanks in advance for any help..,
Assaf

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