[BioC] how to add gene name in limma

[Gaj Stan (BIGCAT)]

Hi,

Sorry for the delayed response (sickness). 

After examining the read.imagene function, I noticed that it extracts
the following annotation (if you 'forget' to call the
annotation-parameter) from an Imagene filename:

            RG$genes <- obj[, c("Field", "Meta Row", "Meta Column", 
                "Row", "Column", "Gene ID")]
 
It seems that the read.maimages-function does something extra with the
data retrieved from read.imagenes, so I'm not so sure to go only for the
read.imagene function (although read.imagenes appears to be creating all
the necessary information as well (-; ).

I noticed in your previous mail that you wanted to extract an annotation
column called "Annotation 1" as well. Perhaps if the above works fine,
you can change adjust the code to grab it as well. A dirty approach, I
agree, but it could solve your problem!

If the above won't work you can follow a last-resort option where you
first try to read your datafiles with read.maimages, followed by
extracting your annotation from a tab-delimited file (containing only
the annotation information in the correct order) (read.table) and put
that into the correct class in your RG$genes (as.dataframe).

Hope that these suggestions solves your problem!

Best wishes,

   Stan


-----Original Message-----
From: john seers (IFR) [mailto:john.seers at bbsrc.ac.uk] 
Sent: 26 September 2006 16:11
To: Gaj Stan (BIGCAT); Bing Zhang
Cc: bioconductor at stat.math.ethz.ch
Subject: RE: [BioC] how to add gene name in limma



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
 

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e-mail john.seers at bbsrc.ac.uk                         
e-disclaimer at http://www.ifr.ac.uk/edisclaimer/ 
 
Web sites:

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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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