[BioC] Some problems in combining ExpressionSet objects with the combine() function

Wed Jul 27 18:04:33 CEST 2011

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' è stato creato con R versione 2.13.1
> 2: il pacchetto 'time' è stato creato con R versione 2.13.1
> 3: il pacchetto 'xtable' è stato creato con R versione 2.13.1
> 4: il pacchetto 'metaMA' è stato creato con R versione 2.13.1
> 5: il pacchetto 'SMVar' è stato creato con R versione 2.13.1
> 6: il pacchetto 'gtools' è stato creato con R versione 2.13.1
> 7: il pacchetto 'gplots' è stato creato con R versione 2.13.1
> 8: il pacchetto 'gdata' è stato creato con R versione 2.13.1
> 9: il pacchetto 'caTools' è 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 