[BioC] Limma - GenePix

[Gordon K Smyth]

Dear Juana,

Once the file has been processed by ArrayExpress, and the header removed, 
the file is no longer a valid GPR format file.  You therefore use 
format="generic" and supply the column names, just as you've done.  I 
expect what you give below will work, but you can easily confirm by trying 
it.

Best wishes
Gordon

> Date: Tue, 23 Jun 2009 13:53:19 +0000
> From: Juana Arco <luana_arch at hotmail.com>
> Subject: [BioC] Limma - GenePix
> To: <bioconductor at stat.math.ethz.ch>
> Message-ID: <SNT109-W62CE4E25CE69389A9BF63EFF360 at phx.gbl>
> Content-Type: text/plain
>
> Hi,
> Can
> anybody help me with this?
> 1)
> I've
> downloaded from the ArrayExpress some GenePix files that don't have
> headers. Because of that I had to read the files (.txt extension for
> some reason) this way:
>
> RG <-
> read.maimages(targets$Filename, columns=list(Rf="GenePix:F635
> Mean",Gf="GenePix:F532 Mean",Rb="GenePix:B635
> Median",Gb="GenePix:B532 Median"), sep="\t",
> path="./")
>
> Is this correct?
>
> 2) I had to
> create the targets files from a file provided by arrayexpress which
> looked something like this:
>
>
>
> SlideNumber	Source
> Name	Label	FileName
> 1	8CT	Cy5	1348628744.txt
> 2	5Exp	Cy3	1348628729.txt
> 3	10Exp	Cy5	1348628754.txt
> 4	4CT	Cy3	1348628724.txt
> 5	1Exp	Cy5	1348628709.txt
> 6	12Exp	Cy5	1348628764.txt
> 7	6Exp	Cy5	1348628734.txt
> 8	3CT	Cy3	1348628719.txt
> 9	13Exp	Cy3	1348628769.txt
> 10	7Exp	Cy3	1348628739.txt
> 11	2CT	Cy5	1348628714.txt
> 12	11Exp	Cy3	1348628759.txt
> 13	9Exp	Cy5	1348628749.txt
> 14	14CT	Cy3	1348628774.txt
>
>
>
> And
> my target file looks like this
>
>
>
> SlideNumber	Filename	Cy3	Cy5
> 1	1348628744.txt	case	control
> 2	1348628729.txt	case	control
> 3	1348628754.txt	control	case
> 4	1348628724.txt	control	case
> 5	1348628709.txt	control	case
> 6	1348628764.txt	control	case
> 7	1348628734.txt	control	case
> 8	1348628719.txt	control	case
> 9	1348628769.txt	case	control
> 10	1348628739.txt	case	control
> 11	1348628714.txt	case	control
> 12	1348628759.txt	case	control
> 13	1348628749.txt	control	case
> 14	1348628774.txt	control	case
>
> Is
> this correct?
> Luana