[BioC] Scaling sRNA/degradome libraries - edgeR

[Atul Kakrana]

Hi List,

I am trying to scale (sRNA/degradome) libraries for specific downstream
analysis. The analysis is different from finding differentially
expressed genes and therefore I might not be using any other function of
edgeR. To scale two libraries:

files =c('Lib1.txt','Lib2.txt')
data <- readDGE(files)
factors.TMM <- calcNormFactors(data,method=c("TMM"))
factors.TMM

This gives me an output:
> factors.TMM
An object of class "DGEList"
$samples
        files lib.size norm.factors
Lib1 Lib1.txt 37075389    0.8146845
Lib2 Lib2.txt 29579135    1.2274690

$counts
                                  Lib1 Lib2
TTTTGCATGGCACTGTTTTGACGCT            2    2
GCCGCTCCCGCCGCCGCGAATCCC             1    0
GACCGAATTACACCCCCGAACTTA             3    1
GCAATGCCGCTTGTAAAGCTCTTTCGTCGAGTG    1    0
GCAAATGGTGGCCGGAACTCAGCAC            1    0
16110540 more rows ...


I see that the counts above are not 'scaled'. Could you please tell me
how can I correct the counts using the 'norm.factors' information? Is
there a function that I can use to input 'factors.TMM' and get scaled
counts? If not, is it possible to do calculation manually i.e. without R
function using the information from $samples?

Best

AK