[BioC] Downloading Data from SMD (and reading into limma)

[Gordon Smyth]

Dear Ian,

This is fixed in limma 1.6.12 available from 
http://bioinf.wehi.edu.au/limma. You can now use

RG <- read.maimages(files, source="smd")

for SMD raw data files produced after 9/2003 and

RG <- read.maimages(files, source="smd.old")

for SMD raw data files produced earlier than that.

Gordon

>Jeremy Gollub jgollub at genome.stanford.edu
>Wed Jun 2 17:39:02 CEST 2004

>Hi, Ian -
>
>I'm a newcomer to BioConductor, but I've been working at SMD for quite a
>while now.
>
>SMD changed the headers in these files some time ago (around 9/03).  It's
>possible limma has not caught up.  (We switched from using database field
>names to more human readable headers.)
>
>Also, you've got a "raw data" file containing meta-information at the
>top.  I expect limma deals with this, since it hasn't changed in quite a
>while, but it's conceivable that that's the problem.
>
>You might try removing the meta-information, and then use read.maimages
>again, with and without columns specified.
>
>Perhaps someone more familiar with limma can provide more help from the
>other end.
>
>Cordially,
>
>--
>Jeremy Gollub, Ph.D.
>jgollub at genome.stanford.edu
>(W) 650/736-0075
>
>On Wed, 2 Jun 2004, Ian Jeffery wrote:
>
> > Hi All
> >  I am interested in downloading the Breast cancer data from Zhao et al from
> > SMD.  I have used the following two commands before to download SMD data
> > before
> >
> > Library(limma)
> >
> > G = read.maimages(dir(pattern='*.xls'), source='smd', fill=TRUE,sep='\t')
> >
> >
> > RG = read.maimages((dir(pattern='*.xls')),columns=(list(Rf=Ch1 Intensity
> > (Mean),Gf=Ch2 Intensity (Mean),Rb=Ch1 Intensity (Median),Gb=Ch2 Intensity
> > (Median) )),fill=TRUE)
> >
> >  but when applied to this data I Get the error message
> >
> > Cannot find column heading in image output file
> >
> > I have tried specifying the column headings and using the skip command to
> > rectify the problem but I only get the same error message
> >
> > Has anyone who has had a similar problem downloading data from SMD share
> > their experience and suggest a suitable command.
> >
> >
> > Thanks,
> > Ian
> >
> > Ps Have attached a reduced version of the file type I am having difficulty
> > with.
> > Abstract and data for the paper can be found at
> > 
> http://genome-www5.stanford.edu/cgi-bin/publication/viewPublication.pl?pub_n
> > o=322