Question: error while using genefilter's nsFilter: could not find function "hgug4112a.db_dbconn"
0
gravatar for Massimo Pinto
10.0 years ago by
Massimo Pinto390
Massimo Pinto390 wrote:
Greetings all, I have finally come across to genefilter's nsFIlter(); it looks like it's going to do quite a lot for me in just one call. I called it as follows: > esetGSEA <- nsFilter(esetPROC, require.entrez=TRUE, require.GOBP=TRUE, remove.dupEntrez=TRUE, var.func=IQR, var.cutoff=0.5) Error in do.call(paste(chip, "_dbconn", sep = ""), list()) : could not find function "hgug4112a.db_dbconn" > annotation(esetPROC) [1] "hgug4112a.db" here's some info on my session: > sessionInfo() R version 2.10.0 (2009-10-26) x86_64-apple-darwin9.8.0 locale: [1] C attached base packages: [1] grid tcltk stats graphics grDevices utils datasets methods base other attached packages: [1] affy_1.24.0 gplots_2.7.3 caTools_1.10 bitops_1.0-4.1 gdata_2.6.1 gtools_2.6.1 [7] hgug4112a.db_2.3.5 org.Hs.eg.db_2.3.6 RSQLite_0.7-3 DBI_0.2-4 Agi4x44PreProcess_1.5.1 genefilter_1.28.0 [13] annotate_1.24.0 AnnotationDbi_1.7.20 limma_3.2.1 Biobase_2.6.0 loaded via a namespace (and not attached): [1] affyio_1.13.5 preprocessCore_1.7.9 splines_2.10.0 survival_2.35-7 tools_2.10.0 xtable_1.5-5 Thanks a lot, Yours Massimo Massimo Pinto Post Doctoral Research Fellow Enrico Fermi Centre and Italian Public Health Research Institute (ISS), Rome http://claimid.com/massimopinto
hgug4112a • 914 views
ADD COMMENTlink modified 10.0 years ago by rgentleman5.5k • written 10.0 years ago by Massimo Pinto390
Answer: error while using genefilter's nsFilter: could not find function "hgug4112a.db_d
0
gravatar for James W. MacDonald
10.0 years ago by
United States
James W. MacDonald51k wrote:
Hi Massimo, Massimo Pinto wrote: > Greetings all, > > I have finally come across to genefilter's nsFIlter(); it looks like > it's going to do quite a lot for me in just one call. I called it as > follows: > >> esetGSEA <- nsFilter(esetPROC, require.entrez=TRUE, require.GOBP=TRUE, remove.dupEntrez=TRUE, var.func=IQR, var.cutoff=0.5) > Error in do.call(paste(chip, "_dbconn", sep = ""), list()) : > could not find function "hgug4112a.db_dbconn" This could probably use a better error message. The problem is that you don't have the annotation package for this chip available, so you cannot filter based on things like Entrez Gene, GO BP, etc. I assume this is a custom chip, so you will need to get the annotation file from Affy and build an annotation package yourself using SQLForge. See the SQLForge vignette for more information: http://www.bioconductor.org/packages/release/bioc/vignettes/Annotation Dbi/inst/doc/SQLForge.pdf Best, Jim > >> annotation(esetPROC) > [1] "hgug4112a.db" > > here's some info on my session: > >> sessionInfo() > R version 2.10.0 (2009-10-26) > x86_64-apple-darwin9.8.0 > > locale: > [1] C > > attached base packages: > [1] grid tcltk stats graphics grDevices utils > datasets methods base > > other attached packages: > [1] affy_1.24.0 gplots_2.7.3 caTools_1.10 > bitops_1.0-4.1 gdata_2.6.1 gtools_2.6.1 > [7] hgug4112a.db_2.3.5 org.Hs.eg.db_2.3.6 RSQLite_0.7-3 > DBI_0.2-4 Agi4x44PreProcess_1.5.1 > genefilter_1.28.0 > [13] annotate_1.24.0 AnnotationDbi_1.7.20 limma_3.2.1 > Biobase_2.6.0 > > loaded via a namespace (and not attached): > [1] affyio_1.13.5 preprocessCore_1.7.9 splines_2.10.0 > survival_2.35-7 tools_2.10.0 xtable_1.5-5 > > Thanks a lot, > Yours > Massimo > > Massimo Pinto > Post Doctoral Research Fellow > Enrico Fermi Centre and Italian Public Health Research Institute (ISS), Rome > http://claimid.com/massimopinto > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > 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
ADD COMMENTlink written 10.0 years ago by James W. MacDonald51k
Hi, I think Massimo is using a custom chip and has prepared it using SQLForge: hgug4112a.db_2.3.5 is present in the sessionInfo(). The solution is to remove the '.db' from the annotation of your ExpressionSet, here is an example with sample data: Best, J. library("Biobase") data(sample.ExpressionSet) print(annotation(sample.ExpressionSet)) ##[1] "hgu95av2" library("hgu95av2.db") library('genefilter') esetPROC <- sample.ExpressionSet esetGSEA <- nsFilter(esetPROC, require.entrez=TRUE, require.GOBP=TRUE, remove.dupEntrez=TRUE, var.func=IQR, var.cutoff=0.5) ## ok print(esetGSEA$filter.log) ##$numLowVar ##[1] 119 ## ##$numDupsRemoved ##[1] 24 ## ##$feature.exclude ##[1] 19 ## ##$numNoGO.BP ##[1] 53 ##$numRemoved.ENTREZID ##[1] 166 annotation(esetPROC) <- "hgu95av2.db" esetGSEA <- nsFilter(esetPROC, require.entrez=TRUE, require.GOBP=TRUE, remove.dupEntrez=TRUE, var.func=IQR, var.cutoff=0.5) ##not ok ##Error in do.call(paste(chip, "_dbconn", sep = ""), list()) : ## could not find function "hgu95av2.db_dbconn" sessionInfo() R version 2.10.0 (2009-10-26) i486-pc-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] genefilter_1.28.0 hgu95av2.db_2.3.5 org.Hs.eg.db_2.3.6 [4] RSQLite_0.7-3 DBI_0.2-4 AnnotationDbi_1.8.0 [7] Biobase_2.6.0 loaded via a namespace (and not attached): [1] annotate_1.24.0 splines_2.10.0 survival_2.35-7 tools_2.10.0 [5] xtable_1.5-5 James W. MacDonald wrote: > Hi Massimo, > > Massimo Pinto wrote: >> Greetings all, >> >> I have finally come across to genefilter's nsFIlter(); it looks like >> it's going to do quite a lot for me in just one call. I called it as >> follows: >> >>> esetGSEA <- nsFilter(esetPROC, require.entrez=TRUE, >>> require.GOBP=TRUE, remove.dupEntrez=TRUE, var.func=IQR, var.cutoff=0.5) >> Error in do.call(paste(chip, "_dbconn", sep = ""), list()) : >> could not find function "hgug4112a.db_dbconn" > > This could probably use a better error message. The problem is that you > don't have the annotation package for this chip available, so you cannot > filter based on things like Entrez Gene, GO BP, etc. > > I assume this is a custom chip, so you will need to get the annotation > file from Affy and build an annotation package yourself using SQLForge. > See the SQLForge vignette for more information: > > http://www.bioconductor.org/packages/release/bioc/vignettes/Annotati onDbi/inst/doc/SQLForge.pdf > > > Best, > > Jim > > >> >>> annotation(esetPROC) >> [1] "hgug4112a.db" >> >> here's some info on my session: >> >>> sessionInfo() >> R version 2.10.0 (2009-10-26) >> x86_64-apple-darwin9.8.0 >> >> locale: >> [1] C >> >> attached base packages: >> [1] grid tcltk stats graphics grDevices utils >> datasets methods base >> >> other attached packages: >> [1] affy_1.24.0 gplots_2.7.3 caTools_1.10 >> bitops_1.0-4.1 gdata_2.6.1 gtools_2.6.1 >> [7] hgug4112a.db_2.3.5 org.Hs.eg.db_2.3.6 RSQLite_0.7-3 >> DBI_0.2-4 Agi4x44PreProcess_1.5.1 >> genefilter_1.28.0 >> [13] annotate_1.24.0 AnnotationDbi_1.7.20 limma_3.2.1 >> Biobase_2.6.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.13.5 preprocessCore_1.7.9 splines_2.10.0 >> survival_2.35-7 tools_2.10.0 xtable_1.5-5 >> >> Thanks a lot, >> Yours >> Massimo >> >> Massimo Pinto >> Post Doctoral Research Fellow >> Enrico Fermi Centre and Italian Public Health Research Institute >> (ISS), Rome >> http://claimid.com/massimopinto >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 10.0 years ago by James F. Reid610
Answer: error while using genefilter's nsFilter: could not find function "hgug4112a.db_d
0
gravatar for rgentleman
10.0 years ago by
rgentleman5.5k
United States
rgentleman5.5k wrote:
Hi Robert Gentleman On Oct 30, 2009, at 7:11 AM, Massimo Pinto <pintarello at="" gmail.com=""> wrote: > Greetings all, > > I have finally come across to genefilter's nsFIlter(); it looks like > it's going to do quite a lot for me in just one call. I called it as > follows: > >> esetGSEA <- nsFilter(esetPROC, require.entrez=TRUE, >> require.GOBP=TRUE, remove.dupEntrez=TRUE, var.func=IQR, >> var.cutoff=0.5) > Error in do.call(paste(chip, "_dbconn", sep = ""), list()) : > could not find function "hgug4112a.db_dbconn" > >> annotation(esetPROC) > [1] "hgug4112a.db" > This is probably part of the problem Drop the .db suffix it is not part of the annotation. You should Use "hgug4112a" > here's some info on my session: > >> sessionInfo() > R version 2.10.0 (2009-10-26) > x86_64-apple-darwin9.8.0 > > locale: > [1] C > > attached base packages: > [1] grid tcltk stats graphics grDevices utils > datasets methods base > > other attached packages: > [1] affy_1.24.0 gplots_2.7.3 caTools_1.10 > bitops_1.0-4.1 gdata_2.6.1 gtools_2.6.1 > [7] hgug4112a.db_2.3.5 org.Hs.eg.db_2.3.6 RSQLite_0.7-3 > DBI_0.2-4 Agi4x44PreProcess_1.5.1 > genefilter_1.28.0 > [13] annotate_1.24.0 AnnotationDbi_1.7.20 limma_3.2.1 > Biobase_2.6.0 > > loaded via a namespace (and not attached): > [1] affyio_1.13.5 preprocessCore_1.7.9 splines_2.10.0 > survival_2.35-7 tools_2.10.0 xtable_1.5-5 > > Thanks a lot, > Yours > Massimo > > Massimo Pinto > Post Doctoral Research Fellow > Enrico Fermi Centre and Italian Public Health Research Institute > (ISS), Rome > http://claimid.com/massimopinto > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 10.0 years ago by rgentleman5.5k
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