Dear list, I am trying to build a Nimblegen platform package using makePlatformDesign. Nimblagen technical support provide me the .xys file for this platform but when I try to build the package the software give me this error: > makePDpackage("60merProbeSeqs.ndf", "1140102_532.xys", manufacturer = > "nimblegen") nimblegen expression The package will be called pd.60merprobeseqs Reading 60merProbeSeqs.txt Assuming a simple design (NOT multiple-wells). Error in data.frame(X = ndfdata$X, Y = ndfdata$Y, feature_set_name = ndfdata$SEQ_ID, : arguments imply differing number of rows: 0, 392247 In addition: Warning messages: 1: no non-missing arguments to max; returning -Inf in: max(ndfdata$X) 2: no non-missing arguments to max; returning -Inf in: max(ndfdata$Y) 3: no non-missing arguments to max; returning -Inf in: max(ndfdata$Y) > I check the number of lines in the .ndf, it is 372776 but the number of lines in the .xys is 392247. How can I solve this problem? Regards Rene'

is this an expression array and are you sure the XYS corresponds to the NDF you have? b On Jul 11, 2007, at 4:42 AM, Rene Dreos ((JIC)) wrote: > Dear list, > I am trying to build a Nimblegen platform package using > makePlatformDesign. Nimblagen technical support provide me the .xys > file > for this platform but when I try to build the package the software > give > me this error: > >> makePDpackage("60merProbeSeqs.ndf", "1140102_532.xys", manufacturer = >> "nimblegen") > nimblegen expression > The package will be called pd.60merprobeseqs Reading > 60merProbeSeqs.txt > Assuming a simple design (NOT multiple-wells). > Error in data.frame(X = ndfdata$X, Y = ndfdata$Y, feature_set_name = > ndfdata$SEQ_ID, : > arguments imply differing number of rows: 0, 392247 In > addition: > Warning messages: > 1: no non-missing arguments to max; returning -Inf in: max(ndfdata$X) > 2: no non-missing arguments to max; returning -Inf in: max(ndfdata$Y) > 3: no non-missing arguments to max; returning -Inf in: max(ndfdata$Y) >> > > I check the number of lines in the .ndf, it is 372776 but the > number of > lines in the .xys is 392247. > How can I solve this problem? > Regards > Rene' > > _______________________________________________ > 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

Hi Rene, Since we've never made a design called "60merProbeSeqs", I suspect that you're working with a file that has been filtered somehow, possibly to include only the experimental probes. If you check the header line of the .xys file, there is a tag/value pair with the name of the design used to create the file. That's the one you need to use makePDpackage. Todd -- Todd Richmond NimbleGen Systems, Inc. Manager of Research Informatics One Science Court Madison, WI 53711 1-608-218-7600 > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor- > bounces at stat.math.ethz.ch] On Behalf Of Rene Dreos (JIC) > Sent: Wednesday, July 11, 2007 3:43 AM > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] Nimblegen chip analysis > > Dear list, > I am trying to build a Nimblegen platform package using > makePlatformDesign. Nimblagen technical support provide me the .xys file > for this platform but when I try to build the package the software give > me this error: > > > makePDpackage("60merProbeSeqs.ndf", "1140102_532.xys", manufacturer = > > "nimblegen") > nimblegen expression > The package will be called pd.60merprobeseqs Reading 60merProbeSeqs.txt > Assuming a simple design (NOT multiple-wells). > Error in data.frame(X = ndfdata$X, Y = ndfdata$Y, feature_set_name = > ndfdata$SEQ_ID, : > arguments imply differing number of rows: 0, 392247 In addition: > Warning messages: > 1: no non-missing arguments to max; returning -Inf in: max(ndfdata$X) > 2: no non-missing arguments to max; returning -Inf in: max(ndfdata$Y) > 3: no non-missing arguments to max; returning -Inf in: max(ndfdata$Y) > > > > I check the number of lines in the .ndf, it is 372776 but the number of > lines in the .xys is 392247. > How can I solve this problem? > Regards > Rene' > > _______________________________________________ > 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