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 -------------- next part -------------- A non-text attachment was scrubbed... Name: 18195.xls Type: application/vnd.ms-excel Size: 20992 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040602/9200fc76/18195.xls

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@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 >