[BioC] Re: limma package

[Gordon Smyth]

At 07:28 AM 3/10/2003, Hua Weng wrote:
>Hi, all:
>
>I'm trying to read in intensity data in limma package. But I get the 
>following error:
>
> > files <- dir(pattern="*\\.gpr")
> > RG <- read.maimages(files, source="genepix")
>Error in read.maimages(files, source = "genepix") :
>         Cannot find column heading in image output file
>
>I don't know what does this error mean. The gpr files I try to load are 
>from GenePix Pro 4.0.1.17, the wavelength I chose for Cy5/Cy3 are 647/546. 
>Do I need to specify these information and How?

Yes you do. Your wavelengths are not the usual so you need to specify them:

RG <- read.maimages(files, columns=list(Rf = "F647 Mean", Gf = "F546 Mean", 
Rb = "B647 Median", Gb = "B546 Median")

Gordon

>Thanks,
>Hua