[BioC] Limma - GenePix

[Gordon K Smyth]

Yes, exactly.  By file header, I mean the information read by 
readGPRHeader().

Gordon

On Thu, 25 Jun 2009, john seers (IFR) wrote:

>
> Hi All
>
> Ah!. Perhaps, "the header removed" does not mean removing the header
> row. Just the n lines of Genepix information?
>
>
>
> Regards
>
>
> John
>
>
>
>
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Gordon K
> Smyth
> Sent: 25 June 2009 08:09
> To: Juana Arco
> Cc: Bioconductor mailing list
> Subject: [BioC] Limma - GenePix
>
> 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
>
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