Hello - thanks also for this second clarification. I actually read this 
help line, but it
was a bit obscure to me

Let me try to summarize:

 > colSums*(**cpm(currentDiff$counts)*) , where currentDiff is a DGEList 
object after normalization

LT1C  LT2C  LT3C  ST2C  ST4C ST10C ST12C  ST5C  ST7C  ST8C ST11C LT1P
LT2P  LT3P  ST2P ST10P ST12P  ST7P  ST8P  ST4P

1e+06 1e+06 1e+06 1e+06 1e+06 1e+06 1e+06 1e+06 1e+06 1e+06 1e+06 1e+06
1e+06 1e+06 1e+06 1e+06 1e+06 1e+06 1e+06 1e+06

==> the *count **matrix (matrix of cpm)* in this case does not use the 
values normalized by library size,
so the values add up to 1 million, correct ? in this case, though, I can 
compare directly values between
samples.

 > colSums(*cpm(currentDiff)*)

LT1C    LT2C    LT3C    ST2C    ST4C   ST10C   ST12C ST5C    ST7C
ST8C   ST11C    LT1P    LT2P    LT3P    ST2P

1421292 1064057  981465  889765  960819  921314  985099  991736 1160034
1144623 1517511  864691 1220229  961164  937648

   ST10P ST12P    ST7P    ST8P    ST4P

  837525 999688  881438  922050  818447

==> these are the same count values, but normalized by library sizes, so 
the CPM will not add up to 1.000.000 (roughly)
per sample, correct ? this is also the way in which CPM are extracted in 
the manual.

But I don't understand one thing: we scale up (or don't scale up) the 
libraries by size, then we calculate the CPM.
Still the CPM should add up to 1 million for each sample in the two 
categories, so that every gene can be compared
directly between samples

Am I missing something fundamental here or the scaling is done *after* 
the CPM calculation ?

Let me know, cheers,

Alessandro

PS

A naive question: what is the role (roughly) for pesudocounts ?

Many thanks for your feedback,

Alessandro & Co.

--

Dear Alessandro,

I see that Devon Ryan has answered your question, but the answer is also 
available directly from the help system.  If you type help("cpm") the 
first line of Details says:

"CPM or RPKM values are useful descriptive measures for the expression 
level of a gene or transcript. By default, the normalized library sizes 
are used in the computation for DGEList objects but simple column sums 
for matrices."

Best wishes
Gordon





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