
Hi Robert,
Thanks so much for the explanation and the solution. The enrichment analysis ran perfectly well.
I was wondering if there is a way to generate FDR-corrected p-values for the KS statistics; that way for each sample we could assess the probability of its association with a gene set.
 
Thanks once again.
 
Best Regards,
Som.
 

> Subject: RE: [BioC] GSVA: using Entrez ID's as identifiers
> From: robert.castelo@upf.edu
> To: genome1976@hotmail.com
> CC: bioconductor@r-project.org
> Date: Thu, 17 Nov 2011 18:31:11 +0100
> 
> hi Som, thanks for the information.
> 
> even though you are not running the latest version of R with the latest
> version of the package, the problem does not seem to be related to that
> fact and i'm able reproduce it with the latest version of both things.
> in any case, it is always good to try to work with the last version of
> all the software.
> 
> the short answer to your question is: try to call the gsva() function
> this way (i'm using below the command line you put on your first email):
> 
> c3gsc2 <- geneIds(c3gsc2)
> 
> new <- gsva(data.m, c3gsc2, abs.ranking=TRUE, min.sz=1, max.sz=Inf,
> no.bootstraps=0, bootstrap.percent = .632, parallel.sz=0,
> parallel.type="SOCK", verbose=TRUE, mx.diff=TRUE)
> 
> the long answer is that, in principle, there is no method on gsva() to
> accept a call with the expression data as a matrix and the gene set as a
> GeneSetCollection object. When the expression data comes as a matrix the
> gene sets should come as a list, which is what we achieve in the line
> i've added before the call to gsva() by transforming the
> GeneSetCollection object into a list object. Under such a circumstance
> you should have got a more informative error saying something like there
> is no such gsva() method that accepts "matrix" and "GeneSetCollection",
> which is something that we should definitely add at some point to the
> package. Instead the method that accepts "matrix" and "list" is
> triggered but it breaks at the first line of code that tries to operate
> on the list of gene sets because that is not a gene list. This strange
> behavior comes from the (strange for me) fact that a GeneSetCollection
> object qualifies also as a list, for instance:
> 
> library(GSVAdata)
> data(c2BroadSets)
> class(c2BroadSets)
> [1] "GeneSetCollection"
> attr(,"package")
> [1] "GSEABase"
> is.list(c2BroadSets)
> [1] TRUE
> 
> anyway, let me know if the fix i propose you above does not work.
> 
> thanks,
> robert.
> 
> On Thu, 2011-11-17 at 09:38 -0500, somnath bandyopadhyay wrote:
> > Hi Robert,
> > 
> > Following is the information you asked for: 
> > 
> > > traceback()
> > 7: match(x, y)
> > 6: na.omit(match(x, y))
> > 5: FUN(X[[1L]], ...)
> > 4: lapply(gset.idx.list, function(x, y) na.omit(match(x, y)),
> > rownames(expr))
> > 3: .local(expr, gset.idx.list, ...)
> > 2: gsva(data.m, c3gsc2, abs.ranking = TRUE, min.sz = 1, max.sz = Inf, 
> > no.bootstraps = 0, bootstrap.percent = 0.632, parallel.sz = 0, 
> > parallel.type = "SOCK", verbose = TRUE, mx.diff = TRUE)
> > 1: gsva(data.m, c3gsc2, abs.ranking = TRUE, min.sz = 1, max.sz = Inf, 
> > no.bootstraps = 0, bootstrap.percent = 0.632, parallel.sz = 0, 
> > parallel.type = "SOCK", verbose = TRUE, mx.diff = TRUE)
> > > sessionInfo ()
> > R version 2.13.1 (2011-07-08)
> > Platform: i386-pc-mingw32/i386 (32-bit)
> > locale:
> > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
> > States.1252 LC_MONETARY=English_United States.1252
> > LC_NUMERIC=C 
> > [5] LC_TIME=English_United States.1252 
> > attached base packages:
> > [1] stats graphics grDevices utils datasets methods
> > base 
> > other attached packages:
> > [1] GSVA_1.0.1 RColorBrewer_1.0-5 limma_3.8.3
> > genefilter_1.34.0 GSEABase_1.14.0 graph_1.30.0
> > annotate_1.30.1 
> > [8] AnnotationDbi_1.14.1 Biobase_2.12.2 
> > loaded via a namespace (and not attached):
> > [1] DBI_0.2-5 RSQLite_0.10.0 splines_2.13.1
> > survival_2.36-10 tools_2.13.1 XML_3.4-2.2 xtable_1.6-0 
> > 
> > 
> > Looking forward to your reply.
> > 
> > Best Regards,
> > Som.
> > 
> > 
> > > Date: Wed, 16 Nov 2011 22:04:06 +0100
> > > From: robert.castelo@upf.edu
> > > To: genome1976@hotmail.com
> > > CC: bioconductor@r-project.org
> > > Subject: Re: [BioC] GSVA: using Entrez ID's as identifiers
> > > 
> > > hi Som,
> > > 
> > > i'm cc'ing the BioC mailing list, please remember to do it when you 
> > > answer since this works as a knowledge base for everyone else.
> > > 
> > > i'd need two bits of information from you to find out what might be 
> > > happening: one, right after the error pops up, please write in the R
> > shell:
> > > 
> > > traceback()
> > > 
> > > and paste here the output of this function.
> > > 
> > > two, please paste also here the ouput of
> > > 
> > > sessionInfo()
> > > 
> > > 
> > > both steps are in fact recommended by the BioC mailinglist posting
> > guide:
> > > 
> > > http://www.bioconductor.org/help/mailing-list/posting-guide
> > > 
> > > robert.
> > > 
> > > On 11/16/11 9:04 PM, somnath bandyopadhyay wrote:
> > > > Hi Robert,
> > > >
> > > > I am trying to use GSVA on a microarray dataset and I am trying to
> > use
> > > > one of the Broad gene set collections for the enrichment purposes.
> > > >
> > > >
> > > > library(GSEABase)
> > > > library(Biobase)
> > > > library(genefilter)
> > > > library(limma)
> > > > library(RColorBrewer)
> > > > library(graph)
> > > > library(GSVA)
> > > >
> > > > c3gsc2 <-
> > > >
> > getGmt("c2.cp.kegg.v3.0.entrez.gmt",collectionType=BroadCollection(category="c3"),geneIdType=EntrezIdentifier())
> > > > class(c3gsc2)
> > > > c3gsc2
> > > >
> > > > data <- read.table("gsva_infliximab_data.txt", header=T,
> > row.names=1,
> > > > sep="\t")# the data matrix is filtered for low expressors etc. and
> > I am
> > > > using Entrez Gene ID as row identifiers.
> > > > class(data)
> > > > data.m <- as.matrix(data)
> > > >
> > > > new <- gsva(data.m,
> > > >
> > c3gsc2,abs.ranking=TRUE,min.sz=1,max.sz=Inf,no.bootstraps=0,bootstrap.percent
> > > >
> > = .632,parallel.sz=0,parallel.type="SOCK",verbose=TRUE,mx.diff=TRUE)
> > > >
> > > >
> > > > I keep getting the following error at this step
> > > > Error in match(x, y) : 'match' requires vector arguments
> > > >
> > > > Could you pleaase tell me what I am doing wrong?
> > > >
> > > > Thanks so much,
> > > > Som.
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > > From: robert.castelo@upf.edu
> > > > > To: kellert@ohsu.edu
> > > > > Date: Wed, 16 Nov 2011 08:43:48 +0100
> > > > > CC: wendy2.qiao@gmail.com; bioconductor@r-project.org
> > > > > Subject: Re: [BioC] GSVA: using Entrez ID's as identifiers
> > > > >
> > > > > hi Tom,
> > > > >
> > > > > i'm a bit unsure what are you asking in relationship with this
> > thread,
> > > > > but i guess you're interested in creating a custom annotation
> > package.
> > > > > For that purpose i'd recommend you to read through the vignettes
> > of the
> > > > > AnnotationDbi package. i'm not an expert in creating custom
> > annotation
> > > > > packages so if you encounter problems to go ahead i think you
> > should
> > > > > start a new thread with the specific question or problem you
> > want to
> > > > > solve.
> > > > >
> > > > > cheers,
> > > > > robert.
> > > > >
> > > > > On Tue, 2011-11-15 at 14:24 -0800, Tom Keller wrote:
> > > > > > Greetings,
> > > > > > The annotation for the miRNA chip does not seem to have the
> > same
> > > > amount of
> > > > > > information as the hgu95 db. Is there some help available for
> > > > mapping miRNA
> > > > > > probes to their target genes?
> > > > > >
> > > > > > thanks
> > > > > > Thomas (Tom) Keller, PhD
> > > > > > kellert at ohsu.edu
> > > > > > 503.494.2442
> > > > > > 6588 R Jones Hall (BSc/CROET)
> > > > > > MMI DNA Services
> > > > > > Member of OHSU Shared Resources
> > > > > >
> > > > > > On Nov 14, 2011, at 11:28 PM, Robert Castelo wrote:
> > > > > >
> > > > > > > hi Wendy,
> > > > > > >
> > > > > > > i'm afraid you need to get a little bit acquainted with the
> > way
> > > > in which
> > > > > > > annotations are handled in BioC. a good starting point could
> > be
> > > > looking
> > > > > > > a the vignette "AnnotationDbi: How to use the .db annotation
> > > > packages"
> > > > > > > from the AnnotationDbi package.
> > > > > > >
> > > > > > > the short answer to your problem is that hgu95a is not the
> > only
> > > > platform
> > > > > > > for which annotations exist in BioC, basically there is an
> > annotation
> > > > > > > package for each platform supported by BioC (you can look
> > all of
> > > > them up
> > > > > > > by going to
> > > > http://www.bioconductor.org/packages/release/BiocViews.html
> > > > > > > and clicking on "AnnotationData") but in order to use on
> > such
> > > > annotation
> > > > > > > packages you need
> > > > > > >
> > > > > > > 1. install it once in your system via source() and
> > biocLite() just as
> > > > > > > with every software package
> > > > > > >
> > > > > > > 2. load it via the library() function.
> > > > > > >
> > > > > > > in order to use the human organism-level package i mentioned
> > in my
> > > > > > > previous email you need to install it first and then load it
> > > > prior to do
> > > > > > > anything else with it.
> > > > > > >
> > > > > > > let me know if this still does not solve your problem.
> > > > > > >
> > > > > > > cheers,
> > > > > > > robert.
> > > > > > >
> > > > > > > On Mon, 2011-11-14 at 18:40 -0500, Wendy Qiao wrote:
> > > > > > >> Hi Robert,
> > > > > > >>
> > > > > > >> Thank you for your reply. I happened to convert all the
> > genes to
> > > > > > >> hgu95a probe IDs as I found that this is the only platform
> > that
> > > > works
> > > > > > >> with ExpressionSet. It would be great that we could make
> > the
> > > > entrez ID
> > > > > > >> works. Following is my error that I got with your code.
> > > > > > >>
> > > > > > >>
> > > > > > >> Thank you.
> > > > > > >> Wendy
> > > > > > >>
> > > > > > >>
> > > > > > >>> BcellSet
> > > > > > >> ExpressionSet (storageMode: lockedEnvironment)
> > > > > > >> assayData: 12148 features, 7 samples
> > > > > > >> element names: exprs
> > > > > > >> protocolData: none
> > > > > > >> phenoData
> > > > > > >> sampleNames: Illumi_PREBCEL_1 Illumi_PREBCEL_2 ...
> > Affy_PREBCEL_4 (7
> > > > > > >> total)
> > > > > > >> varLabels: CellType Platform Replicates
> > > > > > >> varMetadata: labelDescription
> > > > > > >> featureData: none
> > > > > > >> experimentData: use 'experimentData(object)'
> > > > > > >> Annotation: org.Hs.eg.db
> > > > > > >>>
> > > > > > >>
> > > >
> > preBcell.KEGG<-gsva(BcellSet,KEGGc2BroadSets,abs.ranking=FALSE)$es.obs
> > > > > > >> Mapping identifiers between gene sets and feature names
> > > > > > >> Error in GeneSetCollection(lapply(what, mapIdentifiers,
> > to, ...,
> > > > > > >> verbose = verbose)) :
> > > > > > >> error in evaluating the argument 'object' in selecting a
> > method for
> > > > > > >> function 'GeneSetCollection': Error in get(mapName, envir =
> > pkgEnv,
> > > > > > >> inherits = FALSE) :
> > > > > > >> object 'org.Hs.egENTREZID' not found
> > > > > > >>
> > > > > > >>
> > > > > > >>
> > > > > > >>
> > > > > > >> On 14 November 2011 12:27, Robert Castelo
> > <robert.castelo@upf.edu>
> > > > > > >> wrote:
> > > > > > >> hi Wendy,
> > > > > > >>
> > > > > > >> sorry for my late answer. in principle there is no problem
> > for
> > > > > > >> the
> > > > > > >> gsva() function to take Entrez IDs in your expression data
> > > > > > >> matrix.
> > > > > > >>
> > > > > > >> if the expression data comes as a matrix, and rows are
> > > > > > >> annotated with
> > > > > > >> Entrez IDs and the gene sets are also annotated with Entrez
> > > > > > >> IDs, there
> > > > > > >> should be absolutely no problem.
> > > > > > >>
> > > > > > >> if the expression data comes as an ExpressionSet object
> > where
> > > > > > >> the
> > > > > > >> 'features' are not Affy probe IDs but just EntrezIDs. just
> > > > > > >> make sure
> > > > > > >> that the annotation slot has the corresponding
> > organism-level
> > > > > > >> package.
> > > > > > >> for instance, in the case of human:
> > > > > > >>
> > > > > > >> annotation(eset) <- "org.Hs.eg.db"
> > > > > > >>
> > > > > > >> let me know if you have any problem with this.
> > > > > > >>
> > > > > > >> cheers,
> > > > > > >> robert.
> > > > > > >>
> > > > > > >> On Fri, 2011-11-11 at 14:44 -0500, Wendy Qiao wrote:
> > > > > > >>> Hi all,
> > > > > > >>>
> > > > > > >>> I am using the GSVA package for some analysis. I found
> > that
> > > > > > >> the package
> > > > > > >>> only takes the gene expression matrix annotated with
> > > > > > >> affymetrix probe IDs,
> > > > > > >>> although the gene set collection is made of Entrez IDs. I
> > > > > > >> imagine there a
> > > > > > >>> step in the package for converting the Affymetrix probe
> > IDs
> > > > > > >> to Entrez IDs.
> > > > > > >>> As my data are from the Illumina platform, I am wondering
> > if
> > > > > > >> an expression
> > > > > > >>> matrix annotated with Entrez IDs can be used directly.
> > > > > > >>>
> > > > > > >>> Thank you,
> > > > > > >>> Wendy
> > > > > > >>>
> > > > > > >>
> > > > > > >>> [[alternative HTML version deleted]]
> > > > > > >>>
> > > > > > >>> _______________________________________________
> > > > > > >>> Bioconductor mailing list
> > > > > > >>> Bioconductor@r-project.org
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> > > > > > >>> Search the archives:
> > > > > > >>
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> > > > > > >>>
> > > > > > >>
> > > > > > >>
> > > > > > >>
> > > > > > >>
> > > > > > >
> > > > > > > _______________________________________________
> > > > > > > Bioconductor mailing list
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> > > > > >
> > > > > >
> > > > >
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> > 
> 
> 
 		 	   		  
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