[BioC] how to add gene name in limma

[john seers (IFR)]

Hi

Looking at the read.maimages script/code I think perhaps it does not
handle the annotation values. It tests for "imagene" and then calls
"read.imagene" without passing on the annotation values. (I may be wrong
on this - I am not sure what the "..." does). Anyway - my suggestion is
to try calling "read.imagene" directly specifying the annotation
parameter.


Code from read.maimages:

   if (source2 == "imagene") 
        return(read.imagene(files = files, path = path, ext = ext, 
            names = names, columns = columns, wt.fun = wt.fun, 
            verbose = verbose, sep = sep, quote = quote, ...))


Regards


J





 
---

John Seers
Institute of Food Research
Norwich Research Park
Colney
Norwich
NR4 7UA
 

tel +44 (0)1603 251497
fax +44 (0)1603 507723
e-mail john.seers at bbsrc.ac.uk                         
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Web sites:

www.ifr.ac.uk   
www.foodandhealthnetwork.com


-----Original Message-----
From: Gaj Stan (BIGCAT) [mailto:Stan.Gaj at BIGCAT.unimaas.nl] 
Sent: 25 September 2006 12:17
To: Bing Zhang
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] how to add gene name in limma


Dear Bing,

You're right to use the annotation-parameter of the read.maimages
function. E.g.:
 
	annotation = c("GeneName","Description","SystematicName")

Normally it should work fine on importing any other columns (case
sensitive!) from your tab-delimited text files into the genelist object.
If this still does not work, could you supply us the actual code that
you used?

Best wishes,

   Stan

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Bing Zhang
Sent: 25 September 2006 10:09
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] how to add gene name in limma


Dear all,

I am using limma to generate a genelist object for imagene file.

when I am using the command "read.maimages()", I want to add the gene
name into

genelist object. I tried to set annotation and other.columns, but it
seems 

none of them worked.

Could anybody tell me how to do that ?



thanks in advance


bing


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