Hi everyone ... i am trying to build an object using ArrayExpress package for an SMD data available at ArrayExpress using the following command data <- ArrayExpress("E-SMDB-1428") but the object is not being created and m getting the following errors Error in nonAB(i, files, path, ph, rawcol, adr, adf, idf) : 2 scanner names are given ( "ScanAlyze" "SMD" ). It is not possible to handle such a case. Try to set the argument 'rawcol' by choosing among the following columns names: "ScanAlyze:RESULT.CH1I_MEAN" "ScanAlyze:RESULT.CH2I_MEAN" "ScanAlyze:RESULT.CH1B_MEDIAN" "ScanAlyze:RESULT.CH2B_MEDIAN" "SMD:RESULT.CH1D_MEAN" "SMD:RESULT.CH2D_MEAN" "ScanAlyze:RESULT.CH1B_MEAN" "ScanAlyze:RESULT.CH2B_MEAN" "ScanAlyze:RESULT.PERGTBCH1I_1SD" "ScanAlyze:RESULT.PERGTBCH2I_1SD" "ScanAlyze:RESULT.PIX_RAT2_MEDIAN" "ScanAlyze:RESULT.TOT_SPIX" "ScanAlyze:RESULT.TOT_BPIX" "ScanAlyze:RESULT.REGR" "ScanAlyze:RESULT.CORR" "ScanAlyze:TOP" "ScanAlyze:BOT" "ScanAlyze:LEFT" "ScanAlyze:RIGHT" "ScanAlyze:RESULT.FLAG" please help me to sort out this problem regards Rohit -- Rohit Farmer M.Tech Bioinformatics Department of Computational Biology and Bioinformatics Jacob School of Biengineering and Biotechnology Sam Higginbottom Institute of Agriculture, Technology and Sciences (Formerly known as Allahabad Agricultural Institute - Deemed University) Allahabad, UP, INDIA - 211 007 Ph. No. 9839845093, 9415261403 e-Mail rohit.farmer@gmail.com Blog http://rohitsspace.blogspot.com [[alternative HTML version deleted]]

Hey, Rohit - I'm rusty on this, but my recollection is: Scanalyze, a microarray image analysis package, produced foreground (CH[12]I_MEAN) and local background (CH[12]B_MEDIAN) intensity values, but not background-subtracted intensities (CH[12]D_MEAN), which were by somewhat odd convention calculated by the Stanford Microarray Database (SMD) as mean foreground minus median background: CH[12]D_MEAN = CH[12]I_MEAN - CH[12]B_MEDIAN The different qualifiers, Scanalyze vs. SMD, indicate the origin of the given value. For signal values, you probably want the "SMD:RESULT.CH[12]D_MEAN" columns - that's what was generally used for further analysis. The rest of the columns are mostly various QC metrics. CORR is probably the most valuable spot quality metric, indicating the cross-channel pixel-to-pixel correlation (1 is good, 0 is very bad, 0.6 was the typical threshold I saw employed). FLAG is set to a non-zero value if the user indicated a problem with the spot, which might or might not be reflected in the other QC metrics. Cordially, - Jeremy On Tue, Jun 8, 2010 at 11:39 PM, Rohit Farmer <rohit.farmer@gmail.com>wrote: > Hi everyone ... i am trying to build an object using ArrayExpress package > for an SMD data available at ArrayExpress using the following command > > data <- ArrayExpress("E-SMDB-1428") > > but the object is not being created and m getting the following errors > > Error in nonAB(i, files, path, ph, rawcol, adr, adf, idf) : > 2 scanner names are given ( "ScanAlyze" "SMD" ). It is not possible to > handle such a case. Try to set the argument 'rawcol' by choosing among the > following columns names: > "ScanAlyze:RESULT.CH1I_MEAN" > "ScanAlyze:RESULT.CH2I_MEAN" > "ScanAlyze:RESULT.CH1B_MEDIAN" > "ScanAlyze:RESULT.CH2B_MEDIAN" > "SMD:RESULT.CH1D_MEAN" > "SMD:RESULT.CH2D_MEAN" > "ScanAlyze:RESULT.CH1B_MEAN" > "ScanAlyze:RESULT.CH2B_MEAN" > "ScanAlyze:RESULT.PERGTBCH1I_1SD" > "ScanAlyze:RESULT.PERGTBCH2I_1SD" > "ScanAlyze:RESULT.PIX_RAT2_MEDIAN" > "ScanAlyze:RESULT.TOT_SPIX" > "ScanAlyze:RESULT.TOT_BPIX" > "ScanAlyze:RESULT.REGR" > "ScanAlyze:RESULT.CORR" > "ScanAlyze:TOP" > "ScanAlyze:BOT" > "ScanAlyze:LEFT" > "ScanAlyze:RIGHT" > "ScanAlyze:RESULT.FLAG" > > please help me to sort out this problem > > regards > > Rohit > > -- > Rohit Farmer > M.Tech Bioinformatics > Department of Computational Biology and Bioinformatics > Jacob School of Biengineering and Biotechnology > Sam Higginbottom Institute of Agriculture, Technology and Sciences > (Formerly known as Allahabad Agricultural Institute - Deemed University) > Allahabad, UP, INDIA - 211 007 > Ph. No. 9839845093, 9415261403 > e-Mail rohit.farmer@gmail.com > Blog http://rohitsspace.blogspot.com > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Jeremy Gollub jeremy@gollub.net [[alternative HTML version deleted]]