Question: GO Term Enrichment Analysis for ath1121501
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6.9 years ago by
Guest User12k
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Iam trying to do a enrichment analysis and working with data from ath1121501 (arabidopsis) arrays.I have problems in defining the universe and the selected genes though I referred to a number of documentations: My data is as follows: myd #str(myd) chr [1:22810] "244901_at" "244902_at" "244903_at" "244904_at" "244905_at" "244906_at" ... wolunilist# set of selected genes(DEG): str(wolunilist) chr [1:831] "244901_at" "244910_s_at" "245000_at" "245001_at" "245002_at" "245003_at" ... The coding I used was : locus <- unlist(get(myd, ath1121501ACCNUM)) selected<-unlist(get(wolunilist,ath1121501ACCNUM)) params <- new("GOHyperGParams", geneIds = selected, universeGeneIds = locus, annotation="ath1121501", + ontology = "MF", pvalueCutoff = 0.5, conditional = FALSE, testDirection = "over") hgOver <- hyperGTest(params) And I get the following error: debugging in: getUniverseHelper(probes, datPkg, entrezIds) debug: { univ <- unique(unlist(mget(probes, ID2EntrezID(datPkg)))) if (!missing(entrezIds) && !is.null(entrezIds) && length(entrezIds) > 0) univ <- intersect(univ, unlist(entrezIds)) if (length(univ) < 1) stop("After filtering, there are no valid IDs that can be used as the Gene universe.\n Check input values to confirm they are the same type as the central ID used by your annotation package.\n For chip packages, this will still mean the central GENE identifier used by the package (NOT the probe IDs).") univ } I tried several possibilities but did not succeed. -- output of sessionInfo(): R version 2.15.2 (2012-10-26) Platform: i686-redhat-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] annaffy_1.28.0 KEGG.db_2.7.1 GO.db_2.7.1 GOstats_2.22.0 graph_1.34.0 [6] Category_2.22.0 ath1121501.db_2.7.1 org.At.tair.db_2.7.1 RSQLite_0.10.0 DBI_0.2-5 [11] AnnotationDbi_1.18.4 BiocInstaller_1.4.9 limma_3.12.3 affy_1.34.0 Biobase_2.16.0 [16] BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affyio_1.22.0 annotate_1.34.1 genefilter_1.38.0 GSEABase_1.18.0 [5] IRanges_1.14.4 preprocessCore_1.18.0 RBGL_1.32.1 splines_2.15.2 [9] stats4_2.15.2 survival_2.36-14 tools_2.15.2 XML_3.9-4 [13] xtable_1.6-0 zlibbioc_1.2.0 -- Sent via the guest posting facility at bioconductor.org.
annotation go ath1121501 probe • 777 views
ADD COMMENTlink modified 6.9 years ago • written 6.9 years ago by Guest User12k
Answer: GO Term Enrichment Analysis for ath1121501
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6.9 years ago by
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James W. MacDonald51k wrote:
Hi Suganya, On 11/19/2012 6:41 AM, suganya [guest] wrote: > Iam trying to do a enrichment analysis and working with data from ath1121501 (arabidopsis) arrays.I have problems in defining the universe and the selected genes though I referred to a number of documentations: > > My data is as follows: > myd #str(myd) > chr [1:22810] "244901_at" "244902_at" "244903_at" "244904_at" "244905_at" "244906_at" ... > > wolunilist# set of selected genes(DEG): str(wolunilist) > chr [1:831] "244901_at" "244910_s_at" "245000_at" "245001_at" "245002_at" "245003_at" ... > > > The coding I used was : > locus<- unlist(get(myd, ath1121501ACCNUM)) > selected<-unlist(get(wolunilist,ath1121501ACCNUM)) Note that get() assumes you are passing in a single ID. You want mget(). Best, Jim > params<- new("GOHyperGParams", geneIds = selected, universeGeneIds = locus, annotation="ath1121501", > + ontology = "MF", pvalueCutoff = 0.5, conditional = FALSE, testDirection = "over") > hgOver<- hyperGTest(params) > > And I get the following error: > debugging in: getUniverseHelper(probes, datPkg, entrezIds) > debug: { > univ<- unique(unlist(mget(probes, ID2EntrezID(datPkg)))) > if (!missing(entrezIds)&& !is.null(entrezIds)&& length(entrezIds)> > 0) > univ<- intersect(univ, unlist(entrezIds)) > if (length(univ)< 1) > stop("After filtering, there are no valid IDs that can be used as the Gene universe.\n Check input values to confirm they are the same type as the central ID used by your annotation package.\n For chip packages, this will still mean the central GENE identifier used by the package (NOT the probe IDs).") > univ > } > > I tried several possibilities but did not succeed. > > > > > > > > -- output of sessionInfo(): > > R version 2.15.2 (2012-10-26) > Platform: i686-redhat-linux-gnu (32-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 > [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C > [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] annaffy_1.28.0 KEGG.db_2.7.1 GO.db_2.7.1 GOstats_2.22.0 graph_1.34.0 > [6] Category_2.22.0 ath1121501.db_2.7.1 org.At.tair.db_2.7.1 RSQLite_0.10.0 DBI_0.2-5 > [11] AnnotationDbi_1.18.4 BiocInstaller_1.4.9 limma_3.12.3 affy_1.34.0 Biobase_2.16.0 > [16] BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > [1] affyio_1.22.0 annotate_1.34.1 genefilter_1.38.0 GSEABase_1.18.0 > [5] IRanges_1.14.4 preprocessCore_1.18.0 RBGL_1.32.1 splines_2.15.2 > [9] stats4_2.15.2 survival_2.36-14 tools_2.15.2 XML_3.9-4 > [13] xtable_1.6-0 zlibbioc_1.2.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 6.9 years ago by James W. MacDonald51k
Answer: GO Term Enrichment Analysis for ath1121501
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6.9 years ago by
Guest User12k
Guest User12k wrote:
Hi Suganya, On 11/19/2012 6:41 AM, suganya [guest] wrote: > Iam trying to do a enrichment analysis and working with data from ath1121501 (arabidopsis) arrays.I have problems in defining the universe and the selected genes though I referred to a number of documentations: > > My data is as follows: > myd #str(myd) > chr [1:22810] "244901_at" "244902_at" "244903_at" "244904_at" "244905_at" "244906_at" ... > > wolunilist# set of selected genes(DEG): str(wolunilist) > chr [1:831] "244901_at" "244910_s_at" "245000_at" "245001_at" "245002_at" "245003_at" ... > > > The coding I used was : > locus<- unlist(get(myd, ath1121501ACCNUM)) > selected<-unlist(get(wolunilist,ath1121501ACCNUM)) If I use mget then I get the following error: Error in checkKeys(value, Lkeys(x), x at ifnotfound) : value for "245651_s_at" not found > params<- new("GOHyperGParams", geneIds = selected, universeGeneIds = locus, annotation="ath1121501", > + ontology = "MF", pvalueCutoff = 0.5, conditional = FALSE, testDirection = "over") > hgOver<- hyperGTest(params) > > And I get the following error: > debugging in: getUniverseHelper(probes, datPkg, entrezIds) > debug: { > univ<- unique(unlist(mget(probes, ID2EntrezID(datPkg)))) > if (!missing(entrezIds)&& !is.null(entrezIds)&& length(entrezIds)> > 0) > univ<- intersect(univ, unlist(entrezIds)) > if (length(univ)< 1) > stop("After filtering, there are no valid IDs that can be used as the Gene universe.\n Check input values to confirm they are the same type as the central ID used by your annotation package.\n For chip packages, this will still mean the central GENE identifier used by the package (NOT the probe IDs).") > univ > } > > I tried several possibilities but did not succeed. > > > > > > > -- output of sessionInfo(): > -- output of sessionInfo(): > > R version 2.15.2 (2012-10-26) > Platform: i686-redhat-linux-gnu (32-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 > [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C > [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] annaffy_1.28.0 KEGG.db_2.7.1 GO.db_2.7.1 GOstats_2.22.0 graph_1.34.0 > [6] Category_2.22.0 ath1121501.db_2.7.1 org.At.tair.db_2.7.1 RSQLite_0.10.0 DBI_0.2-5 > [11] AnnotationDbi_1.18.4 BiocInstaller_1.4.9 limma_3.12.3 affy_1.34.0 Biobase_2.16.0 > [16] BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > [1] affyio_1.22.0 annotate_1.34.1 genefilter_1.38.0 GSEABase_1.18.0 > [5] IRanges_1.14.4 preprocessCore_1.18.0 RBGL_1.32.1 splines_2.15.2 > [9] stats4_2.15.2 survival_2.36-14 tools_2.15.2 XML_3.9-4 > [13] xtable_1.6-0 zlibbioc_1.2.0 -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink written 6.9 years ago by Guest User12k
Hi Suganya, On 11/20/2012 2:59 AM, suganya [guest] wrote: > Hi Suganya, > > On 11/19/2012 6:41 AM, suganya [guest] wrote: >> Iam trying to do a enrichment analysis and working with data from ath1121501 (arabidopsis) arrays.I have problems in defining the universe and the selected genes though I referred to a number of documentations: >> >> My data is as follows: >> myd #str(myd) >> chr [1:22810] "244901_at" "244902_at" "244903_at" "244904_at" "244905_at" "244906_at" ... >> >> wolunilist# set of selected genes(DEG): str(wolunilist) >> chr [1:831] "244901_at" "244910_s_at" "245000_at" "245001_at" "245002_at" "245003_at" ... >> >> >> The coding I used was : >> locus<- unlist(get(myd, ath1121501ACCNUM)) >> selected<-unlist(get(wolunilist,ath1121501ACCNUM)) > If I use mget then I get the following error: > > Error in checkKeys(value, Lkeys(x), x at ifnotfound) : > value for "245651_s_at" not found This is the point at which I gently remind you that there are help pages for all R functions, and they are often helpful. Looking at the help page a good idea because a.) asking on a list and waiting for help is highly inefficient, and b.) at some point you have to learn to figure things out for yourself. So, typing ?mget at the R prompt, and choosing the 'Environment-like API for Bimap objects {AnnotationDbi}' from the list that pops up, I find the following on the resulting page: First, mget(x, envir, mode, ifnotfound, inherits) which shows the API for mget(). If I then look further, I find ifnotfound: A value to be used if the key is not found. Only NA is currently supported. Best, Jim > > >> params<- new("GOHyperGParams", geneIds = selected, universeGeneIds = locus, annotation="ath1121501", >> + ontology = "MF", pvalueCutoff = 0.5, conditional = FALSE, testDirection = "over") >> hgOver<- hyperGTest(params) >> >> And I get the following error: >> debugging in: getUniverseHelper(probes, datPkg, entrezIds) >> debug: { >> univ<- unique(unlist(mget(probes, ID2EntrezID(datPkg)))) >> if (!missing(entrezIds)&& !is.null(entrezIds)&& length(entrezIds)> >> 0) >> univ<- intersect(univ, unlist(entrezIds)) >> if (length(univ)< 1) >> stop("After filtering, there are no valid IDs that can be used as the Gene universe.\n Check input values to confirm they are the same type as the central ID used by your annotation package.\n For chip packages, this will still mean the central GENE identifier used by the package (NOT the probe IDs).") >> univ >> } >> >> I tried several possibilities but did not succeed. >> >> >> >> >> >> >> > > > -- output of sessionInfo(): > >> -- output of sessionInfo(): >> >> R version 2.15.2 (2012-10-26) >> Platform: i686-redhat-linux-gnu (32-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 >> [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C >> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] annaffy_1.28.0 KEGG.db_2.7.1 GO.db_2.7.1 GOstats_2.22.0 graph_1.34.0 >> [6] Category_2.22.0 ath1121501.db_2.7.1 org.At.tair.db_2.7.1 RSQLite_0.10.0 DBI_0.2-5 >> [11] AnnotationDbi_1.18.4 BiocInstaller_1.4.9 limma_3.12.3 affy_1.34.0 Biobase_2.16.0 >> [16] BiocGenerics_0.2.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.22.0 annotate_1.34.1 genefilter_1.38.0 GSEABase_1.18.0 >> [5] IRanges_1.14.4 preprocessCore_1.18.0 RBGL_1.32.1 splines_2.15.2 >> [9] stats4_2.15.2 survival_2.36-14 tools_2.15.2 XML_3.9-4 >> [13] xtable_1.6-0 zlibbioc_1.2.0 > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD REPLYlink written 6.9 years ago by James W. MacDonald51k
Answer: GO Term Enrichment Analysis for ath1121501
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6.9 years ago by
Guest User12k
Guest User12k wrote:
Iam trying to do a enrichment analysis and working with data from ath1121501 (arabidopsis) arrays.I have problems in defining the universe and the selected genes though I referred to a number of documentations: My data is as follows: myd #str(myd) chr [1:22810] "244901_at" "244902_at" "244903_at" "244904_at" "244905_at" "244906_at" ... wolunilist# set of selected genes(DEG): str(wolunilist) chr [1:831] "244901_at" "244910_s_at" "245000_at" "245001_at" "245002_at" "245003_at" ... The coding I used was : locus <- unlist(get(myd, ath1121501ACCNUM)) # in this case it only fetches a single id head(locus) [1] "ATMG00640" selected<-unlist(get(wolunilist,ath1121501ACCNUM))# in this case it only fetches a single id head(selected) [1] "ATMG00640" params <- new("GOHyperGParams", geneIds = selected, universeGeneIds = locus, annotation="ath1121501", + ontology = "MF", pvalueCutoff = 0.5, conditional = FALSE, testDirection = "over") hgOver <- hyperGTest(params) And I get the following error: debugging in: getUniverseHelper(probes, datPkg, entrezIds) debug: { univ <- unique(unlist(mget(probes, ID2EntrezID(datPkg)))) if (!missing(entrezIds) && !is.null(entrezIds) && length(entrezIds) > 0) univ <- intersect(univ, unlist(entrezIds)) if (length(univ) < 1) stop("After filtering, there are no valid IDs that can be used as the Gene universe.\n Check input values to confirm they are the same type as the central ID used by your annotation package.\n For chip packages, this will still mean the central GENE identifier used by the package (NOT the probe IDs).") univ } I tried several possibilities : mget(c("244901_at", "244902_at", "244903_at", "244904_at", "244905_at"),ath1121501ACCNUM) I get: $`244901_at` [1] "ATMG00640" $`244902_at` [1] "ATMG00650" $`244903_at` [1] "ATMG00660" $`244904_at` [1] "ATMG00670" $`244905_at` [1] "ATMG00680" sel<-unlist(mget(wolunilist,ath1121501ACCNUM)) Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : value for "245651_s_at" not found I am unable to figure out where am going wrong.If I do for a few ids , Iam able to do but if I store it as a character vector I get the above error. -- output of sessionInfo(): R version 2.15.2 (2012-10-26) Platform: i686-redhat-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] annaffy_1.28.0 KEGG.db_2.7.1 GO.db_2.7.1 GOstats_2.22.0 graph_1.34.0 [6] Category_2.22.0 ath1121501.db_2.7.1 org.At.tair.db_2.7.1 RSQLite_0.10.0 DBI_0.2-5 [11] AnnotationDbi_1.18.4 BiocInstaller_1.4.9 limma_3.12.3 affy_1.34.0 Biobase_2.16.0 [16] BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affyio_1.22.0 annotate_1.34.1 genefilter_1.38.0 GSEABase_1.18.0 [5] IRanges_1.14.4 preprocessCore_1.18.0 RBGL_1.32.1 splines_2.15.2 [9] stats4_2.15.2 survival_2.36-14 tools_2.15.2 XML_3.9-4 [13] xtable_1.6-0 zlibbioc_1.2.0 -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink written 6.9 years ago by Guest User12k
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