[BioC] Limma - GenePix

john seers (IFR) john.seers at bbsrc.ac.uk
Thu Jun 25 09:58:47 CEST 2009


Hi Gordon

I am sure this is going to end up somewhere silly but here goes. :)

>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.  

Yes, understood.

>This means that you have to check first yourself, eg using Excel or a
text editor, to see what 
>column headings the files contain.

But  the files have no headers ...


>limma simply finds the first line in the file  which contains the
required column names

Ditto. No headers.

So, unless they are supplied somehow, how can limma know which column
names to use?

Regards


John




-----Original Message-----
From: Gordon K Smyth [mailto:smyth at wehi.EDU.AU] 
Sent: 25 June 2009 08:48
To: john seers (IFR)
Cc: Juana Arco; Bioconductor mailing list
Subject: RE: [BioC] Limma - GenePix

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
>



More information about the Bioconductor mailing list