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