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