Question

HTSanalyzeR GSEA Error

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Dario Strbenac ★ 1.5k

@dario-strbenac-5916

Last seen 5 hours ago

Australia

Hello, I'm trying to do GSEA with the HTSanalyzeR package and I get a non- descriptive error message. Here is the important part of the code : sets.curated <- getGmt("c2.all.v3.0.entrez.gmt") gsca <- new("GSCA", listOfGeneSetCollections=list(MsigDB=sets.curated), geneList=scores, hits=genes.use) gsca <- preprocess(gsca, species = "Hs", initialIDs = "Entrez.gene") gsca <- analyze(gsca, para = list(pValueCutoff = 0.05, pAdjustMethod = "BH", nPermutations = 100, minGeneSetSize = 10, exponent = 1)) When I call analyze() I get an internal error : -Performing hypergeometric analysis ... Error in as.vector(x) : no method for coercing this S4 class to a vector my gsca object can be downloaded from : http://129.94.136.7/file_dump/dario/gsca.obj > head(scores) 643837 148398 339451 84069 9636 375790 0.2191336 0.1679645 0.2565248 0.6424748 0.3201527 0.2340810 > head(genes.use) [1] "55966" "249" "2048" "9473" "80149" "353500" Also, it would be nice if the hits vector isn't mandatory. Figure 1 of the vignette says the package can be used for " (ii) gene set enrichment analysis (GSEA) for concordant trends of a gene set in one phenotype." However, it seems to be only for designed for genetic screens ("(i) hypergeometric tests for overlap between hits and gene sets"), as not giving a hits vector produces an error. > gsca <- new("GSCA", listOfGeneSetCollections=list(MsigDB=sets.curated), geneList=scores) Error in is.character(para) : 'para' is missing I'm using HTSanalyzeR_2.6.0 in R 2.14.0. -------------------------------------- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia

HTSanalyzeR GSCA HTSanalyzeR GSCA • 1.3k views

ADD COMMENT • link updated 13.0 years ago by Xin Wang ▴ 10 • written 13.0 years ago by Dario Strbenac ★ 1.5k

score 0 · Answer 1 · 2011-11-17

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Xin Wang ▴ 10

@xin-wang-4965

Last seen 10.2 years ago

Hello Dario, [Don't know if it is the right way to reply to bioc list. My first time posting a message here.] First of all, thanks very much for using HTSanalyzeR, and for posting an error when using it. Taking a careful look at your code, you would find that the argument 'listOfGeneSetCollections' is supposed to accept a list of gene set collections (each gene set collection is a list of gene sets). Thus, you need to do this: sets.curated <- getGmt("c2.all.v3.0.entrez.gmt") ##convert to a list of gene sets c2<-geneIds(sets.curated) ##create an object of 'GSCA' gsca <- new("GSCA", listOfGeneSetCollections=list(MsigDB=c2), geneList=scores, hits=genes.use) Then probably you will not get any error when running 'preprocess' and 'analyze'. Please do read the '?GSCA' and 'Appendix B' of the Vignette! Let me know if you still have a problem. Best wishes, Xin NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for ...{{dropped:16}}

ADD COMMENT • link 13.0 years ago Xin Wang ▴ 10

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Thanks. It works now. ---- Original message ---- >Date: Thu, 17 Nov 2011 16:14:46 +0000 >From: Xin Wang <xin.wang at="" cancer.org.uk=""> >Subject: Re: [BioC] HTSanalyzeR GSEA Error >To: "D.Strbenac at garvan.org.au" <d.strbenac at="" garvan.org.au=""> >Cc: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> > >Hello Dario, > >[Don't know if it is the right way to reply to bioc list. My first time posting a message here.] > >First of all, thanks very much for using HTSanalyzeR, and for posting an error when using it. > >Taking a careful look at your code, you would find that the argument 'listOfGeneSetCollections' is supposed to accept a list of gene set collections (each gene set collection is a list of gene sets). >Thus, you need to do this: > >sets.curated <- getGmt("c2.all.v3.0.entrez.gmt") >##convert to a list of gene sets >c2<-geneIds(sets.curated) >##create an object of 'GSCA' >gsca <- new("GSCA", listOfGeneSetCollections=list(MsigDB=c2), >geneList=scores, hits=genes.use) > >Then probably you will not get any error when running 'preprocess' and 'analyze'. > >Please do read the '?GSCA' and 'Appendix B' of the Vignette! Let me know if you still have a problem. > >Best wishes, > >Xin > >NOTICE AND DISCLAIMER >This e-mail (including any attachments) is intended for the above- named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. > >We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. >Cancer Research UK >Registered in England and Wales >Company Registered Number: 4325234. >Registered Charity Number: 1089464 and Scotland SC041666 >Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD. -------------------------------------- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia

ADD REPLY • link 13.0 years ago Dario Strbenac ★ 1.5k