[BioC] Downloading Data from SMD

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.


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

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