[BioC] Downloading Data from SMD (and reading into limma)
smyth at wehi.edu.au
Wed Jun 9 06:13:11 CEST 2004
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.
>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
>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
>Jeremy Gollub, Ph.D.
>jgollub at genome.stanford.edu
>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
> > o=322
More information about the Bioconductor