[BioC] reading data into limma

[Gordon Smyth]

At 03:38 AM 30/07/2003, Straubhaar, Juerg wrote:
>Hi,
>
>I am using two-colour spotted array data which I downloaded from the
>Stanford Microarray Database generated with GenePix 4000B. To read the
>data I use:
>
>  RG<-read.maimages(files, source="genepix", path=".", columns=colList,
>fill=TRUE)

There is no reason why this command should not work if your inputs 'files' 
and 'colList' are specified correctly. Note however that source="genepix" 
has no meaning here. Data from the Stanford Microarray Database are in SMD 
rather than Genepix format, and 'source' is ignored anyway when 'columns' 
is specified.

I would be prepared to give more help if you give the value of 'colList' 
and the first 50 lines of the first data file.

Gordon

>colList is a list of name=value pairs, specifying the forground and
>background intensity columns for the two channels.
>
>This generates an error:
>
>Error in "[<-"(*tmp*, , i, value = NULL) :
>
>         number of items to replace is not a multiple of replacement
>length.
>
>Thank you,
>
>Juerg Straubhaar
>
>         [[alternative HTML version deleted]]

---------------------------------------------------------------------------------------
Dr Gordon K Smyth, Senior Research Scientist, Bioinformatics,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3050, Australia
Tel: (03) 9345 2326, Fax (03) 9347 0852,
Email: smyth at wehi.edu.au, www: http://www.statsci.org