[Bioc-devel] Bug Report - for goseq - for RefSeq Genes track - RefSeq identifiers or Entrez Gene ID ?

[Nadia Davidson]

Hi Sonali,

Thanks for reporting this. I’ve moved away from Entrez IDs for refseq with newer genome versions, as I think goseq should take the refs symbols directly. Documentation still needs to be updated for this.

It’s concerning that you’re seeing this behaviour for hg19, so I’ll look into it. A work around is to use the Entrez IDs and provide goseq with the flag “knownGene” rather than “refGene”.

I’m currently on leave until January, so a fix might be slow.

Cheers,
Nadia.


> On 10 Oct 2015, at 8:15 am, Arora, Sonali <sarora at fredhutch.org> wrote:
> 
> Hi everyone,
> 
> I am using goseq to perform Gene Ontology analysis of RNA-seq data and I 
> think I found the following bug.
> 
> Since my RNA-seq data was aligned using Refseq table - so I need to 
> supply id as "refGene" which are actually EntrezId's from 
> goseq::supportedGeneIDs()
> 
> The bug is - that the internal function(getgo) is expecting refseq 
> identifiers and the external function (goseq) is expecting entrez id's..
> 
> When I use refGene as id ( which is actually an entrez gene ids). I get 
> the following error -
> 
>> pwf = nullp(genes, "hg19", "refGene")
> Loading hg19 length data...
> Warning message:
> In pcls(G) : initial point very close to some inequality constraints
>> GO.wall = goseq(pwf, "hg19", "refGene")
> Fetching GO annotations...
> Error in names(tmp) = rep(names(map), times = as.numeric(summary(map)[,  :
>   attempt to set an attribute on NULL
> 
> 
>  After some debugging, I find that internal function getgo() returns a 
> vector of NULL's using "Entrez Gene Id" as id.
> 
>> go = getgo(names(genes), "hg19", "refGene")
>> head(go)
> $<NA>
> NULL
> 
> $<NA>
> NULL
> 
> $<NA>
> NULL
> 
> $<NA>
> NULL
> 
> $<NA>
> NULL
> 
> $<NA>
> NULL
> 
> The last line of the function goseq::getgo() seems to be the issue..
> 
> Browse[2]> head(names(user2cat))
> [1] "NM_000014" "NM_000015" "NM_000016" "NM_000017" "NM_000018" "NM_000019"
> Browse[2]> head(genes)
> [1] "1"         "100"       "1000"      "10000"     "10001" "100037417"
> Browse[2]> head(user2cat[toupper(genes)])
> $<NA>
> NULL
> 
> $<NA>
> NULL
> 
> $<NA>
> NULL
> 
> $<NA>
> NULL
> 
> $<NA>
> NULL
> 
> $<NA>
> NULL
> 
> If I give the getgo() function refseq identifiers instead of entrez id, 
> then the internal function getgo works - but the nullp function fails as 
> it is still expecting entrez gene id.
> 
>> test_genes <- c(0, 0,1,0,0,0)
>> names(test_genes) =c("NM_000014", "NM_000015", "NM_000016", "NM_000017",
> +                      "NM_000018", "NM_000019")
>> go = getgo(names(test_genes), "hg19", "refGene")
>> names(go)
> [1] "NM_000014" "NM_000015" "NM_000016" "NM_000017" "NM_000018" "NM_000019"
>> pwf = nullp(test_genes, "hg19", "refGene")
> Loading hg19 length data...
> Error in getlength(names(DEgenes), genome, id) :
>   The gene names specified do not match the gene names for genome hg19 
> and ID refGene.
>     Gene names given were: NM_000014, NM_000015, NM_000016, NM_000017, 
> NM_000018, NM_000019, NA, NA, NA, NA
>     Required gene names are: 84251, 113451, 25932, 55707, 55707, 84871, 
> 50651, 55707, 7049, 1629
> 
> A reproducible example -
> 
> # case - 1
> test_genes <- c(0, 0,1,0,0,0)
> names(test_genes) <- c(1,100,1000, 10000, 10001, 100037417)
> go = getgo(names(test_genes), "hg19", "refGene")
> 
> # case -2
> names(test_genes) =c("NM_000014", "NM_000015", "NM_000016", "NM_000017",
>                      "NM_000018", "NM_000019")
> go = getgo(names(test_genes), "hg19", "refGene")
> pwf = nullp(test_genes, "hg19", "refGene")
> 
> 
>> sessionInfo()
> R version 3.2.2 RC (2015-08-09 r68965)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 7 x64 (build 7601) Service Pack 1
> 
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United 
> States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] parallel  stats4    stats     graphics  grDevices utils datasets  
> methods   base
> 
> other attached packages:
>  [1] org.Hs.eg.db_3.2.2    AnnotationDbi_1.31.19 IRanges_2.3.24        
> S4Vectors_0.7.22      Biobase_2.29.1 BiocGenerics_0.15.10  
> goseq_1.21.1          RSQLite_1.0.0
>  [9] DBI_0.3.1             geneLenDataBase_1.5.0 BiasedUrn_1.06.1
> 
> loaded via a namespace (and not attached):
>  [1] XVector_0.9.4              GenomicRanges_1.21.30 
> zlibbioc_1.15.0            GenomicAlignments_1.5.18 
> BiocParallel_1.3.54        lattice_0.20-33
>  [7] GenomeInfoDb_1.5.16        tools_3.2.2 grid_3.2.2                 
> SummarizedExperiment_0.3.9 nlme_3.1-122               mgcv_1.8-7
> [13] lambda.r_1.1.7             futile.logger_1.4.1 
> Matrix_1.2-2               rtracklayer_1.29.28 
> futile.options_1.0.0       bitops_1.0-6
> [19] RCurl_1.95-4.7             biomaRt_2.25.3 
> GO.db_3.2.2                GenomicFeatures_1.21.31 
> Biostrings_2.37.8          Rsamtools_1.21.20
> [25] XML_3.98-1.3
> 
> Please advise.
> 
> Thanks and Regards,
> Sonali.
> 
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