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Dear Mayte, thank you for the feedback. The problem appears to happen in the "combine" method for data frames that is defined in Biobase, this could be because of recent changes there that haven't fully been propagated to matchprobes::combineAffyBatch, where combine of data frames is used. Would it be possible for you to make available everything that is necessary to reproduce your problem (e.g. also abatch1 and abatch2, or any (subset) version of them that produce the problem). The problem you report "unfortunately" doesn't seem to happen for the testdata of the matchprobes package itself: http://www.bioconductor.org/checkResults/2.1/bioc-LATEST/ Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber Mayte Suarez-Farinas ha scritto: > Hi, > > I am using combineAffyBatch function from package matchprobes,but I > got the following error: > > library(matchprobes) > res<-combineAffyBatch(list(abatch1,abatch2), probepkg=c > ("hgu133a2probe","hgu133plus2probe"), newcdf="hgu133andPluscdf", > verbose=TRUE) > Loading required package: hgu133a2probe > package:hgu133a2probe hgu133a2probe > package:hgu133plus2probe hgu133plus2probe > 241837 unique probes in common > Error in alleq(levels(x[[nm]]), levels(y[[nm]])) && alleq(x > [sharedRows, : > invalid 'x' type in 'x && y' > > > sessionInfo() > R version 2.6.0 (2007-10-03) > i386-apple-darwin8.10.1 > > locale: > en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] splines tools stats graphics grDevices utils > datasets methods base > > other attached packages: > [1] hgu133a2probe_2.0.0 hgu133plus2probe_2.0.0 > hgu133plus2cdf_2.0.0 affyQCReport_1.16.0 geneplotter_1.16.0 > [6] lattice_0.16-5 annotate_1.16.0 > AnnotationDbi_1.0.6 RSQLite_0.6-3 DBI_0.2-3 > [11] RColorBrewer_1.0-1 affyPLM_1.14.0 > xtable_1.5-2 simpleaffy_2.14.05 gcrma_2.10.0 > [16] matchprobes_1.10.0 genefilter_1.16.0 > survival_2.34 affy_1.16.0 preprocessCore_1.0.0 > [21] affyio_1.6.1 Biobase_1.16.1 > > loaded via a namespace (and not attached): > [1] KernSmooth_2.22-21 grid_2.6.0

Hi Matye, Wolfgang -- I think the error message is trying to say is that a data frame -- probably from phenoData or featureData of one of the AffyBatch objects abatch1, abatch2 -- contains a column that is a 'factor', and the 'levels' of the two columns do not agree. I'd guess sapply(pData(abatch1), class) might point to the likely problem; you'd have to then look at the levels of the corresponding columns in the pheno- (or perhaps feature-) data, and straighten them out. It could also be that the data frames start off ok (same levels) but in the process of 'combine'ing become messed up. For trouble-shooting, I think you should be able to use 'combine' on the data frames themselves, and not on the entire AffyBatch. > df1 = pData(abatch1) > df2 = pData(abtach2) > combine(df1, df2) Martin Wolfgang Huber <huber at="" ebi.ac.uk=""> writes: > Dear Mayte, > > thank you for the feedback. The problem appears to happen in the > "combine" method for data frames that is defined in Biobase, this could > be because of recent changes there that haven't fully been propagated to > matchprobes::combineAffyBatch, where combine of data frames is used. > > Would it be possible for you to make available everything that is > necessary to reproduce your problem (e.g. also abatch1 and abatch2, or > any (subset) version of them that produce the problem). The problem you > report "unfortunately" doesn't seem to happen for the testdata of the > matchprobes package itself: > http://www.bioconductor.org/checkResults/2.1/bioc-LATEST/ > > Best wishes > Wolfgang > > ------------------------------------------------------------------ > Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber > > Mayte Suarez-Farinas ha scritto: >> Hi, >> >> I am using combineAffyBatch function from package matchprobes,but I >> got the following error: >> >> library(matchprobes) >> res<-combineAffyBatch(list(abatch1,abatch2), probepkg=c >> ("hgu133a2probe","hgu133plus2probe"), newcdf="hgu133andPluscdf", >> verbose=TRUE) >> Loading required package: hgu133a2probe >> package:hgu133a2probe hgu133a2probe >> package:hgu133plus2probe hgu133plus2probe >> 241837 unique probes in common >> Error in alleq(levels(x[[nm]]), levels(y[[nm]])) && alleq(x >> [sharedRows, : >> invalid 'x' type in 'x && y' >> >> >> sessionInfo() >> R version 2.6.0 (2007-10-03) >> i386-apple-darwin8.10.1 >> >> locale: >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] splines tools stats graphics grDevices utils >> datasets methods base >> >> other attached packages: >> [1] hgu133a2probe_2.0.0 hgu133plus2probe_2.0.0 >> hgu133plus2cdf_2.0.0 affyQCReport_1.16.0 geneplotter_1.16.0 >> [6] lattice_0.16-5 annotate_1.16.0 >> AnnotationDbi_1.0.6 RSQLite_0.6-3 DBI_0.2-3 >> [11] RColorBrewer_1.0-1 affyPLM_1.14.0 >> xtable_1.5-2 simpleaffy_2.14.05 gcrma_2.10.0 >> [16] matchprobes_1.10.0 genefilter_1.16.0 >> survival_2.34 affy_1.16.0 preprocessCore_1.0.0 >> [21] affyio_1.6.1 Biobase_1.16.1 >> >> loaded via a namespace (and not attached): >> [1] KernSmooth_2.22-21 grid_2.6.0 > > _______________________________________________ > 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 -- Dr. Martin Morgan, PhD Computational Biology Shared Resource Director Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793

Hi Martin, Huber and BioC Martin was right. Now it works!! thanks very much!! Mayte On Nov 26, 2007, at 10:32 AM, Wolfgang Huber wrote: > > Dear Martin - thank you, that seems > Dear Mayte, please let us know if that solves your problem (then we > don't need to go through the big datafile transfer thing). > Best wishes > Wolfgang > > > > > Martin Morgan ha scritto: >> Hi Matye, Wolfgang -- >> >> I think the error message is trying to say is that a data frame -- >> probably from phenoData or featureData of one of the AffyBatch >> objects >> abatch1, abatch2 -- contains a column that is a 'factor', and the >> 'levels' of the two columns do not agree. I'd guess >> >> sapply(pData(abatch1), class) >> >> might point to the likely problem; you'd have to then look at the >> levels of the corresponding columns in the pheno- (or perhaps >> feature-) data, and straighten them out. It could also be that the >> data frames start off ok (same levels) but in the process of >> 'combine'ing become messed up. >> >> For trouble-shooting, I think you should be able to use 'combine' on >> the data frames themselves, and not on the entire AffyBatch. >> >>> df1 = pData(abatch1) >>> df2 = pData(abtach2) >>> combine(df1, df2) >> >> Martin >> >> >> Wolfgang Huber <huber at="" ebi.ac.uk=""> writes: >> >>> Dear Mayte, >>> >>> thank you for the feedback. The problem appears to happen in the >>> "combine" method for data frames that is defined in Biobase, this >>> could >>> be because of recent changes there that haven't fully been >>> propagated to >>> matchprobes::combineAffyBatch, where combine of data frames is used. >>> >>> Would it be possible for you to make available everything that is >>> necessary to reproduce your problem (e.g. also abatch1 and >>> abatch2, or >>> any (subset) version of them that produce the problem). The >>> problem you >>> report "unfortunately" doesn't seem to happen for the testdata of >>> the >>> matchprobes package itself: >>> http://www.bioconductor.org/checkResults/2.1/bioc-LATEST/ >>> >>> Best wishes >>> Wolfgang >>> >>> ------------------------------------------------------------------ >>> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >>> >>> Mayte Suarez-Farinas ha scritto: >>>> Hi, >>>> >>>> I am using combineAffyBatch function from package matchprobes,but I >>>> got the following error: >>>> >>>> library(matchprobes) >>>> res<-combineAffyBatch(list(abatch1,abatch2), probepkg=c >>>> ("hgu133a2probe","hgu133plus2probe"), newcdf="hgu133andPluscdf", >>>> verbose=TRUE) >>>> Loading required package: hgu133a2probe >>>> package:hgu133a2probe hgu133a2probe >>>> package:hgu133plus2probe hgu133plus2probe >>>> 241837 unique probes in common >>>> Error in alleq(levels(x[[nm]]), levels(y[[nm]])) && alleq(x >>>> [sharedRows, : >>>> invalid 'x' type in 'x && y' >>>> >>>> >>>> sessionInfo() >>>> R version 2.6.0 (2007-10-03) >>>> i386-apple-darwin8.10.1 >>>> >>>> locale: >>>> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>> >>>> attached base packages: >>>> [1] splines tools stats graphics grDevices utils >>>> datasets methods base >>>> >>>> other attached packages: >>>> [1] hgu133a2probe_2.0.0 hgu133plus2probe_2.0.0 >>>> hgu133plus2cdf_2.0.0 affyQCReport_1.16.0 geneplotter_1.16.0 >>>> [6] lattice_0.16-5 annotate_1.16.0 >>>> AnnotationDbi_1.0.6 RSQLite_0.6-3 DBI_0.2-3 >>>> [11] RColorBrewer_1.0-1 affyPLM_1.14.0 >>>> xtable_1.5-2 simpleaffy_2.14.05 gcrma_2.10.0 >>>> [16] matchprobes_1.10.0 genefilter_1.16.0 >>>> survival_2.34 affy_1.16.0 preprocessCore_1.0.0 >>>> [21] affyio_1.6.1 Biobase_1.16.1 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] KernSmooth_2.22-21 grid_2.6.0 >>> _______________________________________________ >>> 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 >> > > > -- > Best wishes > Wolfgang > > ------------------------------------------------------------------ > Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >