Hello bioc user, I have found a new package for the quality analysis and preprocessing of microarray data - xps. Unfortunately it is not so easy to use. I am working with the miRNA microarray from affymetrix. I tried to work according to the xps vignette and everything went just fine, up to the point where I wanted to analyze my own data... First I couldn't create a root file, as there is no explanation as to how to do it. I tried the command miRNA.test <- import.expr.scheme("mirna",filedir=getwd(), schemefile="miRNA-1_0_2Xgain.CDF", probefile="miRNA-1_0_2Xgain_probe.tab", annotfile=miRNA- 1_0.annotations.20090219_annot.csv") but all I am getting is this message: ... Warning: probeset <cre-mir1157-star_st> has NumAtoms=4 and NumCells=4 Warning: probeset <cre-mir1162-star_st> has NumAtoms=4 and NumCells=4 Warning: probeset <cre-mir1165-star_st> has NumAtoms=4 and NumCells=4 Warning: probeset <cre-mir1169-star_st> has NumAtoms=4 and NumCells=4 Warning: probeset <mcmv-mir-m01-2-star_st> has NumAtoms=4 and NumCells=4 Warning: probeset <mcmv-mir-m01-3-star_st> has NumAtoms=4 and NumCells=4 Warning: probeset <mcmv-mir-m01-4-star_st> has NumAtoms=4 and NumCells=4 Warning: probeset <mcmv-mir-m23-2-star_st> has NumAtoms=4 and NumCells=4 Warning: probeset <mcmv-mir-m88-1-star_st> has NumAtoms=4 and NumCells=4 Warning: probeset <mcmv-mir-m108-1-star_st> has NumAtoms=4 and NumCells=4 Warning: probeset <mml-mir-1224-star_st> has NumAtoms=4 and NumCells=4 Warning: probeset <hsa-mir-1226-star_st> has NumAtoms=4 and NumCells=4 Warning: probeset <hsa-mir-1228-star_st> has NumAtoms=4 and NumCells=4 Warning: probeset <hsa-mir-664-star_st> has NumAtoms=4 and NumCells=4 Warning: probeset <mdv1-mir-m9-star_st> has NumAtoms=4 and NumCells=4 Warning: probeset <cfa-mir-219-star_st> has NumAtoms=4 and NumCells=4 <50001> records imported... <52900> records imported...Finished PM/MM statistics: 6703 cells with minimum number of PM/MM pairs: 2 78 cells with maximum number of PM/MM pairs: 47 New dataset <mirna-1_0_2xgain> is added to Content... Importing </home> as <mirna-1_0_2xgain.prb>... Error: Header column must begin with <probe set="" name=""> or <probe set="" id=""> Error: Header line of file <mirna-1_0_2xgain_probe.tab> is not correct ... the file I used here is the *.PSI file from the annotation package of the affymetrix miRNA-1_0_2Xgain (to be used with FlashTag HSR). I just rename the end from PSI into tab. I didn't find any other file Does someone know where I can download the probe data for this array type?* * ... Importing </home> as <mirna-1_0_2xgain.ann>... Warning: Number of lines read <7816> is greater than number of genes <7815> Error: Wrong number of separators in line: 14q-0_st miRNA_v1 Homo sapiens Oct 21, 2008 CDBox =HYPERLINK(http://www- snorna.biotoul.fr/plus.php?id=14q(0) LINK to snoRNABase:14q(0)) 14q(0) chr14:100434010-100434086 (+) 77 TGGACCAATGATGAGACAGTGTTTATGAACAAAAGATCATGATTAATCCAGTTC TGCACAAAACACTGAGGTCCATT Error when reading file <mirna-1_0.annotations.20090219_annot.csv>. Apparently the annotation file is also not good enough. Somehow it count more lines than probes (?). I used here the annotation file for the newer chip of the miRNA (2.0),, which is probably the wrong one, but I just wanted to get it first to work, before I start tweaking with it. Error in import.expr.scheme("mirna", filedir = getwd(), schemefile = "miRNA-1_0_2Xgain.CDF", : error in function 'ImportExprSchemes' I am not exactly sure where I can find the right files for this package. A Google search found this site: http://microarray.bu.edu/~sshen/xps/, where complete root files were set to use. I download the mirna.root file and tried to excute it, but it didn't work either I just keep getting the error message: > mirna.scheme <- root.scheme(rootfile="mirna10.root") Warning in <tfile::readstreamerinfo>: mirna10.root: not a TStreamerInfo object Warning in <tfile::readstreamerinfo>: mirna10.root: not a TStreamerInfo object Warning in <tfile::readstreamerinfo>: mirna10.root: not a TStreamerInfo object Warning in <tfile::readstreamerinfo>: mirna10.root: not a TStreamerInfo object It will be nice if anyone has already done something like that and can help me here a little Thanks Assa [[alternative HTML version deleted]]

Dear Assa, First, please note that you can find extensive examples how to create root scheme files in "xps/examples/script4schemes.R". For the miRNA- 1_0 array it has the following information: # directories for Affymetrix library and annotation files libdir <- "/Volumes/GigaDrive/Affy/libraryfiles" anndir <- "/Volumes/GigaDrive/Affy/Annotation" scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes" # miRNA-1_0: # note: you need to rename "miRNA-1_0.probe_list.20081203.txt" to "miRNA-1_0.probe.tab" scheme.mirna10 <- import.expr.scheme("mirna10", filedir = file.path(scmdir, "na31"), schemefile = file.path(libdir, "miRNA-1_0.CDF"), probefile = file.path(libdir, "miRNA- 1_0.probe.tab")) (You can ignore the warning messages you get.) Once you have created file "mirna10.root" you can always load it with: scheme.mirna10 <- root.scheme(paste(scmdir,"mirna10.root",sep="/")) Regarding the new miRNA-2_0 array you need the corresponding "miRNA-2_0.probe.tab" file. Since I could not find this file or the corresponding "miRNA-2_0.probe_list.txt" file on the Affymetrix web site you need to ask Affymetrix from where to obtain this file. Please note that "miRNA-2_0.psi" is not a substitute for a probe.tab file since it does not contain the necessary information. In the future please provide always your sessionInfo(). Best regards Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._ On 3/18/11 4:53 PM, Assa Yeroslaviz wrote: > Hello bioc user, > > I have found a new package for the quality analysis and preprocessing of > microarray data - xps. > Unfortunately it is not so easy to use. > I am working with the miRNA microarray from affymetrix. > > I tried to work according to the xps vignette and everything went just fine, > up to the point where I wanted to analyze my own data... > > First I couldn't create a root file, as there is no explanation as to how to > do it. I tried the command > > miRNA.test<- import.expr.scheme("mirna",filedir=getwd(), > > > schemefile="miRNA-1_0_2Xgain.CDF", > probefile="miRNA-1_0_2Xgain_probe.tab", > annotfile=miRNA- 1_0.annotations.20090219_annot.csv") > > > but all I am getting is this message: > > ... > Warning: probeset<cre-mir1157-star_st> has NumAtoms=4 and NumCells=4 > Warning: probeset<cre-mir1162-star_st> has NumAtoms=4 and NumCells=4 > > Warning: probeset<cre-mir1165-star_st> has NumAtoms=4 and NumCells=4 > Warning: probeset<cre-mir1169-star_st> has NumAtoms=4 and NumCells=4 > Warning: probeset<mcmv-mir-m01-2-star_st> has NumAtoms=4 and NumCells=4 > > Warning: probeset<mcmv-mir-m01-3-star_st> has NumAtoms=4 and NumCells=4 > Warning: probeset<mcmv-mir-m01-4-star_st> has NumAtoms=4 and NumCells=4 > Warning: probeset<mcmv-mir-m23-2-star_st> has NumAtoms=4 and NumCells=4 > > Warning: probeset<mcmv-mir-m88-1-star_st> has NumAtoms=4 and NumCells=4 > Warning: probeset<mcmv-mir-m108-1-star_st> has NumAtoms=4 and NumCells=4 > Warning: probeset<mml-mir-1224-star_st> has NumAtoms=4 and NumCells=4 > > Warning: probeset<hsa-mir-1226-star_st> has NumAtoms=4 and NumCells=4 > Warning: probeset<hsa-mir-1228-star_st> has NumAtoms=4 and NumCells=4 > Warning: probeset<hsa-mir-664-star_st> has NumAtoms=4 and NumCells=4 > > Warning: probeset<mdv1-mir-m9-star_st> has NumAtoms=4 and NumCells=4 > Warning: probeset<cfa-mir-219-star_st> has NumAtoms=4 and NumCells=4 > > <50001> records imported... > <52900> records imported...Finished > PM/MM statistics: > 6703 cells with minimum number of PM/MM pairs: 2 > 78 cells with maximum number of PM/MM pairs: 47 > > > New dataset<mirna-1_0_2xgain> is added to Content... > Importing</home> > as<mirna-1_0_2xgain.prb>... > Error: Header column must begin with<probe set="" name=""> or<probe set="" id=""> > > Error: Header line of file<mirna-1_0_2xgain_probe.tab> is not correct > ... > the file I used here is the *.PSI file from the annotation package of > the affymetrix miRNA-1_0_2Xgain (to be used with FlashTag HSR). I just > rename the end from PSI into tab. I didn't find any other file > > > Does someone know where I can download the probe data for this array type?* > > * > ... > Importing</home> > as<mirna-1_0_2xgain.ann>... > Warning: Number of lines read<7816> is greater than number of genes<7815> > > > Error: Wrong number of separators in line: > 14q-0_st miRNA_v1 Homo sapiens Oct 21, > 2008 CDBox =HYPERLINK(http://www- snorna.biotoul.fr/plus.php?id=14q(0) LINK > to snoRNABase:14q(0)) 14q(0) chr14:100434010-100434086 > (+) 77 TGGACCAATGATGAGACAGTGTTTATGAACAAAAGATCATGATTAATCCAGTTC TGCACAAAACACTGAGGTCCATT > > Error when reading file<mirna-1_0.annotations.20090219_annot.csv>. > > Apparently the annotation file is also not good enough. Somehow it > count more lines than probes (?). > > > I used here the annotation file for the newer chip of the miRNA > (2.0),, which is probably the wrong one, but I just wanted to get it > first to work, before I start tweaking with it. > > Error in import.expr.scheme("mirna", filedir = getwd(), schemefile = > "miRNA-1_0_2Xgain.CDF", : > > > error in function 'ImportExprSchemes' > > > I am not exactly sure where I can find the right files for this package. > A Google search found this site: http://microarray.bu.edu/~sshen/xps/, where > complete root files were set to use. > > I download the mirna.root file and tried to excute it, but it didn't work > either > > I just keep getting the error message: > >> mirna.scheme<- root.scheme(rootfile="mirna10.root") > Warning in<tfile::readstreamerinfo>: mirna10.root: not a TStreamerInfo object > Warning in<tfile::readstreamerinfo>: mirna10.root: not a TStreamerInfo object > Warning in<tfile::readstreamerinfo>: mirna10.root: not a TStreamerInfo object > Warning in<tfile::readstreamerinfo>: mirna10.root: not a TStreamerInfo object > > > It will be nice if anyone has already done something like that and can help > me here a little > > Thanks > Assa > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >