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Hi Ingrid -- I think > Error in is.null(x) || all.equal(x, y, check.attr = FALSE) : > invalid 'y' type in 'x || y' is coming from Biobase, where it is trying to combine data.frame's, probably from phenoData objects. Probably there is a name mismatch between the sample names identified in the dataFile and designFile arguments. In general traceback() after the error occurs can give some insight into the nature of the problem; in this case the error is quite obscure and deeply nested, so this might not have been that helpful. An updated version of Biobase should be available via biocLite in a little more than 24 hours time; I made this change earlier, but neglected to commit it to the release branch. Martin Ingrid H. G. ?stensen <ingrid.h.g.ostensen at="" rr-research.no=""> writes: > Hi > > I have got an error when I am using ABarray: > >> eset=ABarray("data.txt", "Heidi_desing.txt", "sampleOrigin") > Using arrayName to match experiment with signal in file: data.txt > The sample names are: > [1] "1" "2" "3" "4" "5" "6" > AssayNames in dataFile: data.txt > [1] "HA004J2_1A_1" "HA004J7_1A_2" "HA004JB_1A_3" "HA004JD_1B_1" "HA004JI_1B_2" "HA004JK_1B_3" "HA004JN_2A_1" "HA004JO_2A_2" "HA004JP_2A_3" "HA004JS_2B_1" "HA004JT_2B_2" "HA004JU_2B_3" > > The following arrays were excluded from analysis: > [1] "HA004JN_2A_1" "HA004JO_2A_2" "HA004JP_2A_3" "HA004JS_2B_1" "HA004JT_2B_2" "HA004JU_2B_3" > Reading data from data.txt ...... > This may take several minutes.... > Finished data reading. > The results will be in the folder: Result_sampleOrigin/ > [1] "Creating plot for Signal Hybridization_Control ..." > [1] "Creating plot for Signal Negative_Control ..." > [1] "Creating plot for Signal IVT_Kit_Control_BIOB ..." > [1] "Creating plot for Signal IVT_Kit_Control_BIOC ..." > [1] "Creating plot for Signal IVT_Kit_Control_BIOD ..." > [1] "Creating plot for Signal RT_Kit_Control_DAP ..." > [1] "Creating plot for Signal RT_Kit_Control_LYS ..." > [1] "Creating plot for Signal RT_Kit_Control_PHE ..." > > Perform basic analysis for non-normalized data ... > [1] "Creating barplot for probes detectable ... QC_DetectableProbeSN3" > Error in is.null(x) || all.equal(x, y, check.attr = FALSE) : > invalid 'y' type in 'x || y' > > > > > I have seen that others have had the same error but could not find a reply to that e-mail. Does any one know what might be wrong? (I also get the same error using R 2.5.1) > > > R version 2.6.0 (2007-10-03) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] tcltk splines tools stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ABarray_1.6.0 multtest_1.18.0 survival_2.34 Biobase_1.16.1 > > > Regards, > Ingrid > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793