Hypergeometric test's summary error while using GOstats

Question

[ciemanek]

Hi! I am trying to perform hypergeometric test to find enriched GO terms among the genes that differ significantly between two clusters. However, I have a problem when I try to get a summary of the hypergeometric test from GOstats package - I get the following error:

Error in initialize(value, ...) : argument "go_id" is missing, with no default

For the annotation I use hgu133plus2.db package (my microarrays are Affymetrix HG U133 + PM) and the way I get to the universe and selected genes' Entrez ID is as follows:

x <- hgu133plus2ENTREZID
mapped_probes <- mappedkeys(x)
universe <- unique(unlist(as.list(x[mapped_probes])))

sig_probes <- rownames(res)[which(res[,3] != 0)] # res is a result of decideTests from limma package so in this line I am picking all the significant genes from the comparison of interest to me

sig_probes <- sub(x = sig_probes, pattern = "_PM_", replacement = "_") # I am changing IDs to match them with IDs in hgu133plus2.db package
significant <- unlist(as.list(x[sig_probes]))
significant <- unique(significant[!is.na(significant)])

# going to the hypergeometric test
params <- new('GOHyperGParams',
              geneIds=significant,
              universeGeneIds=universe,
              ontology='BP',
              pvalueCutoff=0.001,
              conditional=F,
              testDirection='over',
              annotation="hgu133plus2.db")
hgOver <- hyperGTest(params)
result <- summary(hgOver)

I would expect this is some problem with an annotation? Any help regarding what I can be doing wrong will be appreciated.

Agata

Answer 1

[m.dejung]

Hi Agata, I am not sure if you solved your problem, but in my case it was a incompatibility with a newer RSQLite package. So after downgrading it to 2.1.0 everything worked again.

Best Mario

[Vinay]

This is exactly what I did, and it worked!!

Answer 2

[ciemanek]

Hi Mario!

Thanks a lot for your answer. In my case the problem was that my R version was not up to date. The latest topGO works perfectly fine with the newest R version (3.5.0) however at the time when I was perfofming my analysis R 3.5.0 was only available for Windows so I had to switch to my personal laptop from Ubuntu in order to use the latest version of R and Bioconductor.

All the best, Agata

Answer 3

[Dunja]

Hi,

Just wanted to say that I had the same error (due to not having the newest R version) when running summary on hyperGTest output (GOstats), and I solved the problem by downgrading the RSQLite to 2.1.0, as m.dejung suggested. It works now, no errors :)

My session info:

R version 3.4.3 (2017-11-30)

Platform: x86_64-apple-darwin15.6.0 (64-bit)

Running under: macOS Sierra 10.12.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] GO.db_3.5.0 GOstats_2.44.0 graph_1.56.0
[4] Category_2.44.0 Matrix_1.2-12 AnnotationDbi_1.40.0 [7] IRanges_2.12.0 S4Vectors_0.16.0 Biobase_2.38.0
[10] BiocGenerics_0.24.0 RSQLite_2.1.0

loaded via a namespace (and not attached): [1] Rcpp_0.12.17 splines_3.4.3 bit_1.1-14
[4] xtable_1.8-2 lattice_0.20-35 blob_1.1.1
[7] tools_3.4.3 grid_3.4.3 AnnotationForge_1.20.0 [10] DBI_1.0.0 genefilter_1.60.0 survival_2.42-4
[13] RBGL_1.54.0 yaml_2.1.19 bit64_0.9-7
[16] digest_0.6.15 GSEABase_1.40.1 Rgraphviz_2.22.0
[19] bitops_1.0-6 RCurl_1.95-4.10 memoise_1.1.0
[22] compiler_3.4.3 XML_3.98-1.11 annotate_1.56.2
[25] pkgconfig_2.0.1

Best Dunja

[Vinay]

As I commented earlier in "m.dejung's" response, this procedure (downgrading the RSQLite to 2.1.0) definitely worked for me as well.