[BioC] Downloading Data from SMD

[Jeremy Gollub]

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
>