Question: Problem With Hypergtest On Hgu133Plus2 Data
gravatar for juulia.suvilehto
8.5 years ago by
juulia.suvilehto0 wrote:

I'm trying to run a hyperGTest from GOstats (bioconductor) package on human genome data and keep getting error messages as detailed below.

The data is from hgu133plus2 and the R commands I ran (slightly paraphrased for clarity and length) are

gen <- read.table("path/genes_hum.txt", sep="\t",stringsAsFactors=FALSE, header=TRUE)
genes <- unlist(gen)

params <- new("GOHyperGParams", annotation="hgu133plus2.db", geneIds = genes, universeGeneIds = unique(toTable(hgu133plus2ENTREZID)[,2]), ontology = "BP", pvalueCutoff = 0.05, conditional = FALSE, testDirection = "over")

Results <- hyperGTest(params)

First I kept getting the following error :

Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0061377" not found Calls: summary ... keys<- -> keys<- -> Lkeys<- -> Lkeys<- -> .checkKeys

(though the faulty GO accession was occasionally "GO:2000142" or "GO:0072677", depending on genes selected for gene set).

Them internets often attributed this to outdated packages, so I updated all R packages that I've assumed relevant (namely AnnotationDbi, GO.db, GOstats, and hgu133plus2.db) and the error changed into

Error in mget(probes, ID2EntrezID(datPkg)) : second argument must be an environment Calls: hyperGTest ... getUniverseViaGo -> getUniverseHelper -> unique -> unlist -> mget

Can someone hint what I'm doing wrong?

Thanks in advance!

[sessionInfo() gives:

R version 2.13.0 (2011-04-13) Platform: i686-pc-linux-gnu (32-bit)

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C

attached base packages: [1] stats graphics grDevices utils
datasets methods base

other attached packages: [1] optparse_0.9.5 getopt_1.17
oligo_1.16.2 [4] preprocessCore_1.14.0 oligoClasses_1.14.0
GOstats_2.22.0 [7] Category_2.18.0 GO.db_2.7.1
GSEABase_1.14.0 [10] graph_1.30.0 annotate_1.30.1
hgu133plus2.db_2.7.1 [13] RSQLite_0.11.1
DBI_0.2-5 [16] AnnotationDbi_1.18.1 Biobase_2.12.2
BiocGenerics_0.2.0 [19] rkward_0.5.4

loaded via a namespace (and not attached): [1] affxparser_1.24.0 affyio_1.20.0 Biostrings_2.20.4 bit_1.1-8 [5] ff_2.2-5
genefilter_1.34.0 IRanges_1.10.6 RBGL_1.28.0 [9] splines_2.13.0 survival_2.36-9 tools_2.13.0 XML_3.9-4
[13] xtable_1.7-0 ]

bioconductor • 3.0k views
ADD COMMENTlink modified 6.9 years ago by Biostar ♦♦ 20 • written 8.5 years ago by juulia.suvilehto0

Please update your R to a current version. Your R version and, subsequently, your Bioconductor packages are almost two years out-of-date.

ADD REPLYlink written 8.5 years ago by Sean Davis26k

Lo and behold! Updating R and Bioconductor solved the problem. Silly me for not thinking of the basics. Thanks for your help!

ADD REPLYlink written 8.5 years ago by juulia.suvilehto0

I love it when that works!

ADD REPLYlink written 8.5 years ago by Sean Davis26k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2560 users visited in the last hour