[BioC] Layout in limma

Gordon Smyth smyth at wehi.edu.au
Wed Feb 11 23:33:30 MET 2004

At 09:09 PM 11/02/2004, Binita Dutta wrote:
>Hi All,
>I have gene description of microarray in text file (not the GAL file as 
>given for the swirl example in limma package) and the data set is also in 
>the text file. As i undertsnad there are no facilities for importing 
>marrayRaw objects into limma.

There are now. See the 'convert' package at 
http://bioinf.wehi.edu.au/limma/convert.html. This package will be added to 
Bioconductor soon, but you can download it from there in the meantime.

>  I want to analyse the whole data in limma for the color flip 
> experiments. I can import the data for analysis in limma package but have 
> not been able to feed in the layout of my array. Please let me know how 
> to do this. I have 2 "grid columns" and 12 "grid rows". Within each grid 
> there are 45 "spot columns" and 21 "spot rows".

I agree that this is not as well documented now as it was in the past, 
since I simplified the commands in the User's Guide. You need 
layout=list(ngrid.r=2,ngrid.c=12,nspot.r=45,nspot.c=21). See 

>  Is there anythng similar to "widget.marrayLayout()" in limma package?

Not exactly, but there is as entire GUI interface to limma available at 


>Thanks in advance.
>Dr. Binita Dutta
>MicroArray Facility(MAF)
>UZ Gasthuisberg
>Onderwijs en Navorsing
>Herestraat 49
>3000 Leuven
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

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