[BioC] Limma - GenePix

[Gordon K Smyth]

Hi John,

I might be missing what you mean ...

To read microarray data in a generic format, you have to tell limma the 
column names of the data columns you want it to read.  This means that you 
have to check first yourself, eg using Excel or a text editor, to see what 
column headings the files contain.

Given a generic format file, limma simply finds the first line in the file 
which contains the required column names, skipping any earlier lines, and 
reads from there.

Best wishes
Gordon

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

> Hi
>
> Just out of curiosity, how does limma know how to match the names? Where
> do the column names come from?
>
> I am missing something here ...
>
> 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
> ne.science.biology.informatics.conductor
>