dear group, i have a dataset from ArrayExpress. According to the authors they used codelink chip with Alexa 647-Streptavidin conjugate. However, the description on ArrayExpress says that the experimenters used Axon instrument for GenePix format. When I try to load in a test file with name, Spot_mean, Bkgd_median, I get an error. The 23 quantitation types that can be selected are: B6351SD,B6352SD,Autoflag,BPixels,B635,B635CV,B635Mean,B635Median,B635S D,Circularity,Dia,FPixels,F635Sat,F635CV,F635Mean,F635MeanB635,F635Med ian,F635MedianB635,F635SD,F635TotalIntensity,Flags,Normalize,SNR635 where ',' is a tab. Out of 23 columns I selected F635Mean and B635Median (Spot_mean, Bkgd_Median respectively). I tried fls = list.files(pattern='TXT',path='.') > fls [1] "cdlink_test.TXT" data <- readCodelink(files=list.files(pattern="TXT"), sample.name=NULL, flag=list(M=NA, I=NA, C=NA), dec=NULL, type="Spot",preserve=FALSE, verbose=2) > data<-readCodelink(fls,sample.name=NULL, flag=list(M=NA, I=NA, C=NA), dec=NULL, type="Spot",preserve=FALSE, verbose=2) Error in readHeader(files[n], dec = TRUE) : Not a Codelink exported file. > Could any one please help me, if this data is processed or raw data. if raw, then what are the errors I am committing. thanks in advance sri URL quantitation types: http://www.ebi.ac.uk/arrayexpress/query/dataselection;jsessionid=41B61 BD0C846519E3B6B4349F8DC96A4?expid=826113654 URL data http://www.ebi.ac.uk/arrayexpress/query/dataselection;jsessionid=41B61 BD0C846519E3B6B4349F8DC96A4?expid=826113654#processed_data

Dear Srinivas, the codelink package currently only supports reading data exported from Codelink Software as text, not other type of data (including exported text from excel files obtained from Codelink Software). I don't know how the data in ArrayExpress is stored and if you can export it in the original format (taking a fast look at the links you provided my guess is no). Can you send me the first 20 lines of one of these files to see if it conforms with the Codelink format? If not, i can only suggest reading the data directly using standard R function such read.table, read.delim, etc. Once you have read it, and you have a matrix of intensity values you can apply directly normalization functions available in other packages as affy or limma. In fact, this is tha way i used to do it initially. Best, D. El 11/04/2006, a las 4:50, Srinivas Iyyer escribi?: > dear group, > i have a dataset from ArrayExpress. According to the > authors they used codelink chip with Alexa > 647-Streptavidin conjugate. However, the description > on ArrayExpress says that the experimenters used Axon > instrument for GenePix format. > > When I try to load in a test file with > name, Spot_mean, Bkgd_median, I get an error. > > > The 23 quantitation types that can be selected are: > B6351SD,B6352SD,Autoflag,BPixels,B635,B635CV,B635Mean,B635Median,B635S > D,Circularity,Dia,FPixels,F635Sat,F635CV,F635Mean,F635MeanB635,F635Med > ian,F635MedianB635,F635SD,F635TotalIntensity,Flags,Normalize,SNR635 > where ',' is a tab. > > Out of 23 columns I selected F635Mean and B635Median > (Spot_mean, Bkgd_Median respectively). I tried > fls = list.files(pattern='TXT',path='.') >> fls > [1] "cdlink_test.TXT" > > data <- readCodelink(files=list.files(pattern="TXT"), > sample.name=NULL, flag=list(M=NA, I=NA, C=NA), > dec=NULL, type="Spot",preserve=FALSE, verbose=2) > > >> data<-readCodelink(fls,sample.name=NULL, > flag=list(M=NA, I=NA, C=NA), dec=NULL, > type="Spot",preserve=FALSE, verbose=2) > Error in readHeader(files[n], dec = TRUE) : > Not a Codelink exported file. >> > > > Could any one please help me, if this data is > processed or raw data. if raw, then what are the > errors I am committing. > > thanks in advance > sri > > URL quantitation types: > http://www.ebi.ac.uk/arrayexpress/query/ > dataselection;jsessionid=41B61BD0C846519E3B6B4349F8DC96A4? > expid=826113654 > > URL data > http://www.ebi.ac.uk/arrayexpress/query/ > dataselection;jsessionid=41B61BD0C846519E3B6B4349F8DC96A4? > expid=826113654#processed_data > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor