Some problems in combining ExpressionSet objects with the combine() function
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@james-w-macdonald-5106
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Hi Manuela, When replying, please use 'reply to all' so the conversation doesn't go off-list. On 7/27/2011 11:23 AM, Manuela Di Russo wrote: > Hi Jim, > I updated my version of BioC, but the problem remains. > I noticed that when I load the MAMA library many messages appear. Among > them there is a message concerning the function combine: Good point. You will want to load affy first, then do the combining, then load MAMA. Best, Jim > > Carico il pacchetto richiesto: 'gdata' > > The following object(s) are masked from 'package:Biobase': > > combine > > Could it be the problem? > I'm sorry if my questions are a little bit stupid but I have a lot to > learn! > Thank you! > Manuela > >> setwd("C:/Documents and Settings/Manu.MA- ANALYSIS2/Desktop/colorectal >> cancer meta-analysis") >> library(MAMA) > Carico il pacchetto richiesto: affy > Carico il pacchetto richiesto: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'browseVignettes()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation("pkgname")'. > > Carico il pacchetto richiesto: GeneMeta > Carico il pacchetto richiesto: genefilter > Carico il pacchetto richiesto: metaArray > Carico il pacchetto richiesto: tspair > Carico il pacchetto richiesto: time > Carico il pacchetto richiesto: xtable > Carico il pacchetto richiesto: metaMA > Carico il pacchetto richiesto: limma > Carico il pacchetto richiesto: SMVar > > Carico il pacchetto richiesto: 'metaMA' > > The following object(s) are masked from 'package:genefilter': > > rowVars > > Carico il pacchetto richiesto: OrderedList > Carico il pacchetto richiesto: twilight > Carico il pacchetto richiesto: splines > Carico il pacchetto richiesto: gtools > > Carico il pacchetto richiesto: 'gtools' > > The following object(s) are masked from 'package:metaArray': > > logit > > Carico il pacchetto richiesto: gplots > Carico il pacchetto richiesto: gdata > gdata: Unable to locate valid perl interpreter > gdata: > gdata: read.xls() will be unable to read Excel XLS and XLSX files > gdata: unless the 'perl=' argument is used to specify the location of a > gdata: valid perl intrpreter. > gdata: > gdata: (To avoid display of this message in the future, please ensure > gdata: perl is installed and available on the executable search path.) > gdata: Unable to load perl libaries needed by read.xls() > gdata: to support 'XLX' (Excel 97-2004) files. > > gdata: Unable to load perl libaries needed by read.xls() > gdata: to support 'XLSX' (Excel 2007+) files. > > gdata: Run the function 'installXLSXsupport()' > gdata: to automatically download and install the perl > gdata: libaries needed to support Excel XLS and XLSX formats. > > Carico il pacchetto richiesto: 'gdata' > > The following object(s) are masked from 'package:Biobase': > > combine > > The following object(s) are masked from 'package:stats': > > nobs > > The following object(s) are masked from 'package:utils': > > object.size > > Carico il pacchetto richiesto: caTools > Carico il pacchetto richiesto: bitops > Carico il pacchetto richiesto: grid > > Carico il pacchetto richiesto: 'gplots' > > The following object(s) are masked from 'package:stats': > > lowess > > Carico il pacchetto richiesto: multtest > > Carico il pacchetto richiesto: 'multtest' > > The following object(s) are masked from 'package:gplots': > > wapply > > Carico il pacchetto richiesto: RankProd > Carico il pacchetto richiesto: annaffy > Carico il pacchetto richiesto: GO.db > Carico il pacchetto richiesto: AnnotationDbi > Carico il pacchetto richiesto: DBI > > Carico il pacchetto richiesto: KEGG.db > > Warning messages: > 1: il pacchetto 'MAMA' ? stato creato con R versione 2.13.1 > 2: il pacchetto 'time' ? stato creato con R versione 2.13.1 > 3: il pacchetto 'xtable' ? stato creato con R versione 2.13.1 > 4: il pacchetto 'metaMA' ? stato creato con R versione 2.13.1 > 5: il pacchetto 'SMVar' ? stato creato con R versione 2.13.1 > 6: il pacchetto 'gtools' ? stato creato con R versione 2.13.1 > 7: il pacchetto 'gplots' ? stato creato con R versione 2.13.1 > 8: il pacchetto 'gdata' ? stato creato con R versione 2.13.1 > 9: il pacchetto 'caTools' ? stato creato con R versione 2.13.1 > library(affy) >> library(limma) >> load(url("http://math.muni.cz/~xihnatov/DataColonHalf.RData")) >> ls() > [1] "australia" "denmark" "japan" >> combine(japan,denmark,australia) > Errore in data.frame(<s4 object="" of="" class="" "expressionset"="">, <s4 object="" of=""> class "ExpressionSet">, : > arguments imply differing number of rows: 41, 77, 36 > Inoltre: Warning message: > closing unused connection 3 > (gzcon(http://math.muni.cz/~xihnatov/DataColonHalf.RData)) >> sessionInfo() > R version 2.13.0 (2011-04-13) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=Italian_Italy.1252 LC_CTYPE=Italian_Italy.1252 > [3] LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C > [5] LC_TIME=Italian_Italy.1252 > > attached base packages: > [1] grid splines stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] MAMA_1.0.2 annaffy_1.24.0 KEGG.db_2.5.0 > [4] GO.db_2.5.0 RSQLite_0.9-4 DBI_0.2-5 > [7] AnnotationDbi_1.14.1 RankProd_2.24.0 multtest_2.8.0 > [10] gplots_2.8.0 caTools_1.12 bitops_1.0-4.1 > [13] gdata_2.8.2 gtools_2.6.2 OrderedList_1.24.0 > [16] twilight_1.28.0 metaMA_1.1 SMVar_1.3.2 > [19] limma_3.8.2 xtable_1.5-6 tspair_1.10.0 > [22] time_1.1 metaArray_1.28.0 GeneMeta_1.24.0 > [25] genefilter_1.34.0 affy_1.30.0 Biobase_2.12.2 > > loaded via a namespace (and not attached): > [1] affyio_1.20.0 annotate_1.30.0 MASS_7.3-12 > [4] MergeMaid_2.24.0 preprocessCore_1.14.0 survival_2.36-5 >> > > > > ----- Original Message ----- From: "James W. MacDonald" > <jmacdon at="" med.umich.edu=""> > To: "Manuela Di Russo" <manuela.dirusso at="" for.unipi.it=""> > Cc: <bioconductor at="" r-project.org=""> > Sent: Wednesday, July 27, 2011 4:42 PM > Subject: Re: [BioC] Some problems in combining ExpressionSet objects > with the combine() function > > >> Hi Manuela, >> >> You don't give the output from sessionInfo(), but I suspect you have >> an outdated version of BioC. >> >> > combine(japan,denmark,australia) >> ExpressionSet (storageMode: lockedEnvironment) >> assayData: 500 features, 154 samples >> element names: exprs >> protocolData: none >> phenoData >> sampleNames: GSM101849 GSM101851 ... GSM327326 (154 total) >> varLabels: position satelite >> varMetadata: labelDescription >> featureData: none >> experimentData: use 'experimentData(object)' >> Annotation: hgu133plus2 >> Warning messages: >> 1: In alleq(levels(x[[nm]]), levels(y[[nm]])) : 2 string mismatches >> 2: data frame column 'satelite' levels not all.equal >> > sessionInfo() >> R version 2.13.0 alpha (2011-03-28 r55140) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C >> [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.iso885915 >> [7] LC_PAPER=en_US.iso885915 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] affy_1.29.3 Biobase_2.11.10 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.19.4 preprocessCore_1.13.6 >> >> Best, >> >> Jim >> >> >> >> On 7/27/2011 10:17 AM, Manuela Di Russo wrote: >>> Hi all, >>> >>> I'm struggling with the meta-analysis of microarray data. In the user >>> guide of the bioconductor package "MAMA" there is an exemple of >>> meta-analysis in cancer microarray data concerning the comparison of >>> expression profiles in MSI (microsatelite instable) and MSS >>> (microsatelite stable) colon cancer. Data are gathered from three >>> microarray experiments from public databases >>> >>> The original data sets have been preprocessed and subsampled (same >>> set of 500 genes). All data sets have been normalized and are in >>> log2-scale. The corresponding sample sizes for the three datasets, >>> named denmark, australia and japan, are 77 (39 MSI and 38 MSS), 36 (5 >>> MSI and 31 MSS) and 41 (16 MSI and 25 MSS), respectively. Each of the >>> datasets is stored as an ExpressionSet object. >>> >>> I would like to perform a meta-analysis combining the three >>> ExpressionSets into one and using the limma package with a convenient >>> design matrix to model the study effect. >>> >>> I have two questions: >>> >>> 1) I tried using the function "combine" in order to combine the three >>> datasets (two by two, too) but I obtain the following error message: >>> >>> library(MAMA) >>> >>> library(affy) >>> >>> load(url("http://math.muni.cz/~xihnatov/DataColonHalf.RData")) >>> >>> ls() >>> >>> data<-combine(australia,denmark,japan) >>> >>> Error in data.frame(<s4 object="" of="" class="" "expressionset"="">,<s4 object="">>> of class "ExpressionSet">, : arguments imply differing number of >>> rows: 36, 77, 41. >>> >>> I checked the function instructions: >>> >>> combine(eSet,eSet): Combine two eSet objects. To be combined, eSets >>> must have identical numbers of featureNames, distinct sampleNames, >>> and identical annotation >>> >>> and the three datasets meet these conditions. >>> >>> So, can someone help me? Is there a problem in the datasets I >>> downloaded? >>> >>> 2) How can I access the code of the function "model.matrix" (package >>> : stats)? Typing the name of the function as I usuallly do seems not >>> to work in this case. Is it a "protected" function? >>> >>> Thank you for your help! >>> >>> Manuela >>> >>> ------------------------------------------------------------------ ---------------------- >>> >>> Manuela Di Russo, Ph.D. Student >>> Department of Experimental Pathology, MBIE >>> University of Pisa >>> Pisa, Italy >>> e-mail: manuela.dirusso at for.unipi.it >>> tel: +39050993538 >>> [[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 >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should >> not be used for urgent or sensitive issues > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
Microarray GO Cancer Colon affy limma Microarray GO Cancer Colon affy limma • 896 views
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