Some problems in combining ExpressionSet objects with the combine() function
1
0
Entering edit mode
@manuela-di-russo-4778
Last seen 6.9 years ago
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@for.unipi.it tel: +39050993538 [[alternative HTML version deleted]]
Microarray Cancer Colon limma Microarray Cancer Colon limma • 1.3k views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 7 hours ago
United States
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
ADD COMMENT

Login before adding your answer.

Traffic: 519 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6