[BioC] GOstats code validation

[James W. MacDonald]

On Monday, September 30, 2013 1:36:36 PM, kaushal Raj Chaudhary [guest] 
wrote:
>
> Dear List,
>
> I am using your package "GOstats" for my gene expression data.  I took seleceted gene id (entrez id) and gene universrse which is all gens in the chip we used (entrez id) form excel file provided by the genome studio software.  Here is the code.  If you have some  available time  I want to you to validate the code .
>
>
>
> setwd("W:/KAUSHAL_RESEARCH/K_Surendaran/Data")
>
> source("http://www.bioconductor.org/biocLite.R")
>
> biocLite("AnnotatidatonDbi")
>
> library("AnnotationDbi")
>
> biocLite("illuminaMousev2.db")
>
> library("illuminaMousev2.db")
>
> biocLite("GOstats")
>
> library("GOstats")
>
> biocLite("KEGG.db")
>
> library("KEGG.db")
>
> biocLite("reactome.db")
>
> library("reactome.db")
>
>
>
> data1=read.csv("uni_id.csv", header=T)   ### gene universe
>
> data2=data.matrix(data1)
>
> colnames(data2)<-NULL
>
> AllID=as.numeric(data2)
>
> head(AllID)
>
>
>
> [1]    212772    212772 100039693     56378     74257     20510
>
>
> data3=read.csv("selec_ID.csv", header=T)  ### selected gene
>
> data4=data.matrix(data3)
>
> colnames(data4)<-NULL
>
> SelecID=as.numeric(data4)
>
> head(SelecID)
>
>
>
> [1]  74257  20322  59010  66398  50995 242864
>
>
> getClass("GOHyperGParams")
>
> getClass("KEGGHyperGParams")
>
>
>
> params<-new("GOHyperGParams", geneIds=SelecID, universeGeneIds=AllID, annotation=c("illuminaMousev2"), ontology="BP", pvalueCutoff=0.01, testDirection="over")
>
> resultBP1<-hyperGTest(params)
>
> resultBP1
>
> summary(resultBP1)
>
> htmlReport(resultBP1, file="ALL_hgo.html")
>
>
>
> Partial output:
> GOBPID 	Pvalue 	OddsRatio 	ExpCount 	Count 	Size 	Term
> GO:0001905 	0.000 	Inf 	0 	2 	2 	activation of membrane attack complex
>
>
>
> I also want to get the genes in the count column.

You can get those genes using probeSetSummary()

Best,

Jim


>
> Thank you very much for help.
>
>
>
>
>   -- output of sessionInfo():
>
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] xtable_1.7-1              GO.db_2.9.0               reactome.db_1.44.0
>   [4] KEGG.db_2.9.1             GOstats_2.26.0            graph_1.38.3
>   [7] Category_2.26.0           illuminaMousev2.db_1.18.0 org.Mm.eg.db_2.9.0
> [10] RSQLite_0.11.4            DBI_0.2-7                 AnnotationDbi_1.22.6
> [13] Biobase_2.20.1            BiocGenerics_0.6.0        BiocInstaller_1.10.3
>
> loaded via a namespace (and not attached):
>   [1] annotate_1.38.0       AnnotationForge_1.2.2 genefilter_1.42.0     GSEABase_1.22.0
>   [5] IRanges_1.18.4        RBGL_1.36.2           splines_3.0.1         stats4_3.0.1
>   [9] survival_2.37-4       tools_3.0.1           XML_3.98-1.1
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099