[BioC] Interspecies differential expression of orthologs with Edger
assaf www
assafwww at gmail.com
Tue Aug 26 23:37:49 CEST 2014
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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