[BioC] Re: concentrations

[Adaikalavan Ramasamy]

Thats because I made a mistake. Omitting the preprocessing step (i.e.
justRMA() code) and then applying pm() and mm() on 'raw' seems to work.

I never looked at signal values before preprocessing stage (which
includes the summary step where the pm and mm values are combined into a
single value), so I am cannot be 100% sure.

BTW, I think you could have debugged what the error message meant by
yourself. Reading help(pm) or help(probeset) would have told you that it
was expecting an object of "Affybatch" class. Find out what class(raw)
and class(out) is and see if you can understand where my mistake was.

Regards, Adai



On Tue, 2005-06-07 at 19:44 +0200, Mohammad Esad-Djou wrote:
> Thank you for your answer. I used your solution. Unfortunately I get error message.
> 
> ramasamy at cancer.org.uk schrieb am 03.06.05 00:29:58:
> > 
> > 
> > I think all you need is something like the below :
> > 
> > spikein.genes <- c("geneA", "geneB", "geneC", "geneD")  # see [1]
> is Ok:
> spikein.genes <- geneNames(data.raw)[1:14]
> Test: 
> > spikein.genes
>  [1] "1007_s_at" "1053_at"   "117_at"    "121_at"    "1255_g_at" "1294_at"
>  [7] "1316_at"   "1320_at"   "1405_i_at" "1431_at"   "1438_at"   "1487_at"
> [13] "1494_f_at" "1598_g_at"
> 
> 
> 
> > raw <- ReadAffy()
> 
> > out <- justRMA(raw)
> 
> out <- justRMA(filenames = file.name) # file.name is 42 CEL file.
> Test:
> > out
> Expression Set (exprSet) with
>         22300 genes
>         42 samples
>                  phenoData object with 1 variables and 42 cases
>          varLabels
>                 sample: arbitrary numbering
> 
> BUT:>>>>
> > pms <- pm(out)[ spikein.genes, ]
> > pms <- pm(out)[spikein.genes,]
> Error in pm(out) : No direct or inherited method for function "pm" for this call
> 
> why?
> 
> Best regards,
> Mohammad
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