combineAffyBatch
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Max Kauer ▴ 140
@max-kauer-2254
Last seen 7.5 years ago
Dear list, I am trying to merge to affybatches with combineAffyBatch from the matchprobes package. One is hgu133a (33 arrays), the other hgu133plus2 (12 arrays). While the example in the vignette works fine, I tried to make the affybatches for my data so it is exactly as in the vignette but I always get an error like this: Loading required package: hgu133aprobe Loading required package: hgu133plus2probe package:hgu133aprobe hgu133aprobe package:hgu133plus2probe hgu133plus2probe 241837 unique probes in common Error in combine(pDataX, pDataY) : data.frames contain conflicting data: non-conforming colname(s): fromFile I would be grateful for any suggestions or if anybody knows another good way to combine the data. Thanks! Max Here's my code: h133a <- list.celfiles() h133plus2 <- list.celfiles() pd1 <- new("AnnotatedDataFrame", data = data.frame(fromFile = I(h133plus2),row.names = paste("f", seq(1:12), sep=""))) pd2 <- new("AnnotatedDataFrame", data = data.frame(fromFile = I(h133a),row.names = paste("f", seq(1:33), sep=""))) h133a.ab <- read.affybatch(filenames = h133a, phenoData = pd2) h133plu2.ab <- read.affybatch(filenames = h133plus2, phenoData = pd1) res <- combineAffyBatch(list(h133a.ab, h133plu2.ab), c("hgu133aprobe", "hgu133plus2probe"), newcdf="hgu133comb", verbose=TRUE) > sessionInfo() R version 2.5.0 (2007-04-23) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "tools" "tcltk" "stats" "graphics" "grDevices" "utils" [7] "datasets" "methods" "base" other attached packages: hgu133plus2probe hgu133aprobe matchprobes affy affyio "1.16.0" "1.16.0" "1.8.1" "1.14.1" "1.4.0" Biobase svGUI svViews svIO svMisc "1.14.0" "0.9-5" "0.9-5" "0.9-5" "0.9-5" R2HTML "1.58"
hgu133a Biobase matchprobes hgu133a Biobase matchprobes • 1.5k views
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@martin-morgan-1513
Last seen 6 weeks ago
United States
Hi Max -- For data.frames, combine makes sure that any cell shared between two data frames (i.e., cells with the same row and column names in each data frame) have the same data. In your example, an example of a shared cell would be pd1["f1", "fromFile"] and pd2["f1", "fromFile"]. Presumable the contents of these cells is different, so there is no sensible way to combine them. A simple solution might be to rename the rows: > pd1 <- data.frame(fromFile = I(LETTERS[1:5]), + row.names = paste("f", seq(1:5))) > pd2 <- data.frame(fromFile = I(letters[1:5]), + row.names = paste("g", seq(1:5))) > res <- combine(pd1, pd2) Martin "Kauer Maximilian Otto" <maximilian.kauer at="" ccri.at=""> writes: > Dear list, > > I am trying to merge to affybatches with combineAffyBatch from the matchprobes package. One is hgu133a (33 arrays), the other hgu133plus2 (12 arrays). > > While the example in the vignette works fine, I tried to make the affybatches for my data so it is exactly as in the vignette but I always get an error like this: > > Loading required package: hgu133aprobe > Loading required package: hgu133plus2probe > package:hgu133aprobe hgu133aprobe > package:hgu133plus2probe hgu133plus2probe > 241837 unique probes in common > Error in combine(pDataX, pDataY) : data.frames contain conflicting data: > non-conforming colname(s): fromFile > > I would be grateful for any suggestions or if anybody knows another good way to combine the data. > > Thanks! > Max > > Here's my code: > > h133a <- list.celfiles() > h133plus2 <- list.celfiles() > pd1 <- new("AnnotatedDataFrame", data = data.frame(fromFile = I(h133plus2),row.names = paste("f", seq(1:12), sep=""))) > pd2 <- new("AnnotatedDataFrame", data = data.frame(fromFile = I(h133a),row.names = paste("f", seq(1:33), sep=""))) > h133a.ab <- read.affybatch(filenames = h133a, phenoData = pd2) > h133plu2.ab <- read.affybatch(filenames = h133plus2, phenoData = pd1) > res <- combineAffyBatch(list(h133a.ab, h133plu2.ab), c("hgu133aprobe", "hgu133plus2probe"), newcdf="hgu133comb", verbose=TRUE) > >> sessionInfo() > R version 2.5.0 (2007-04-23) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] "tools" "tcltk" "stats" "graphics" "grDevices" "utils" > [7] "datasets" "methods" "base" > > other attached packages: > hgu133plus2probe hgu133aprobe matchprobes affy affyio > "1.16.0" "1.16.0" "1.8.1" "1.14.1" "1.4.0" > Biobase svGUI svViews svIO svMisc > "1.14.0" "0.9-5" "0.9-5" "0.9-5" "0.9-5" > R2HTML > "1.58" > > _______________________________________________ > 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 Bioconductor / Computational Biology http://bioconductor.org
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