[BioC] Limma and R

[J.delasHeras at ed.ac.uk]

Quoting VERONICA COSTANTINI <costantini.3 at osu.edu>:

> Hi, I am trying to run limma under R following the User guide.   
> Everything Ok until I get the message at the end, and I can figure   
> out wich one is the error. Could anyone help me?
>
> Thanks
> Veronica
>
>
>> library (limma)
>> dir()
>  [1] "Data GPR"                           "ExpDescFile.xls"
>  [3] "M1.4 VI2.4 (5-10-07) VI"            "M1.8 VI1.8 (5-25-07) VI"
>  [5] "M2.4 VI1.4 (5-10-07) VI"            "M2.8 VI2.8 (5-25-07) VI"
>  [7] "M3.4 VI3.4 (5-10-07) VI"            "M3.8 VI3.8 (5-25-07) VI"
>  [9] "Microarray data -Project M vs V 2"  "Microarray data -Project M vs VI"
> [11] "Microarray data -Project M vs VI 2" "nonM14VI14.gpr"
> [13] "nonM14VI14.txt"                     "nonM18VI18.gpr"
> [15] "nonM24VI24.gpr"                     "nonM28VI28.gpr"
> [17] "nonM34VI34.gpr"                     "nonM38VI38.gpr"
> [19] "PoSaVsample.txt"                    "PoSaVsampleII.txt"
> [21] "Test.xls"                           "Verification"
>> targets <- readTargets("PoSaVsample.txt")
>> ls()
> [1] "targets"
>> targets
>   Slide.Number Name      File.Name   Cy3  Cy5
> 1            1 MV14 nonM14VI14.gpr virus mock
> 2            2 MV24 nonM24VI24.gpr virus mock
> 3            3 MV34 nonM34VI34.gpr virus mock
> 4            4 MV18     nonM18VI18 virus mock
> 5            5 MV28     nonM28VI28 virus mock
> 6            6 MV38     nonM38VI38 virus mock
>> RG <-read.maimages(targets$File.Name, source="genepix")
> Error in RG[[a]][, i] <- obj[, columns[[a]]] :
>         number of items to replace is not a multiple of replacement length


Did you realise that your targets file specifies 3 non-existant files?

nonM18VI18
nonM28VI28
nonM38VI38

don't forget to include the extension (".gpr" in this case).

Jose


-- 
Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
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