[BioC] Re: concentrations

[Mohammad Esad-Djou]

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
_________________________________________________________________________
Mit der Gruppen-SMS von WEB.DE FreeMail können Sie eine SMS an alle