[Bioc-devel] Weird monkey identifiers in org.Hs.eg.db
Aaron Lun
|n||n|te@monkey@@w|th@keybo@rd@ @end|ng |rom gm@||@com
Sat Apr 27 01:21:52 CEST 2019
Thanks Daniel. Glad to see the end of that monkey business, my analyses
were going bananas.
On Fri, Apr 26, 2019 at 3:41 PM Van Twisk, Daniel <
Daniel.VanTwisk using roswellpark.org> wrote:
> I've pushed new 3.8.2 orgdbs that should propagate soon. They do not have
> this issue.
> ------------------------------
> *From:* Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Pages,
> Herve <hpages using fredhutch.org>
> *Sent:* Thursday, April 25, 2019 9:19:35 PM
> *To:* Aaron Lun; Vincent Carey
> *Cc:* Bioc-devel; jmacdon using u.washington.edu
> *Subject:* Re: [Bioc-devel] Weird monkey identifiers in org.Hs.eg.db
>
> Hi Aaron,
>
> On 4/25/19 16:44, Aaron Lun wrote:
>
> It doesn't seem like it - on my installation, org.Hs.eg.db is still...
> monkeying around.
>
>
> __
> w c(..)o (
> \__(-) __)
> /\ (
> /(_)___)
> w /|
> | \
> m m
>
> Daniel has prepared a new batch of *.db0 and org.* packages (v 3.8.1). The
> new packages are on their way and should become available via
> BiocManager::install() in the next 12 hours or so.
>
> Hopefully they'll put an end to the Great Monkey Conspiracy!
>
> Unfortunately we won't see the effect on tomorrow's build report, only on
> Saturday's report.
>
> Cheers,
>
> H.
>
>
>
>
>
> On Thu, Apr 25, 2019 at 9:17 AM Vincent Carey <stvjc using channing.harvard.edu
> ><mailto:stvjc using channing.harvard.edu>
> wrote:
>
>
>
> Has this situation been rectified?
>
> On Tue, Apr 23, 2019 at 11:40 AM Van Twisk, Daniel <
> Daniel.VanTwisk using roswellpark.org<mailto:Daniel.VanTwisk using roswellpark.org>>
> wrote:
>
>
>
> We've made some changes to our annotation generation scripts this release
> and it seems these may have introduced some errors. Thank you for
> identifying this issue and I will try to have some fixes out asap.
>
> ________________________________
> From: Bioc-devel <bioc-devel-bounces using r-project.org><mailto:
> bioc-devel-bounces using r-project.org> on behalf of James
> W. MacDonald <jmacdon using uw.edu><mailto:jmacdon using uw.edu>
> Sent: Tuesday, April 23, 2019 11:03:02 AM
> To: Aaron Lun
> Cc: Bioc-devel
> Subject: Re: [Bioc-devel] Weird monkey identifiers in org.Hs.eg.db
>
> Looks like the ensembl table of the human.db0 package got polluted with
> *Pan
> troglodytes* genes:
>
>
>
> con <- dbConnect(SQLite(),
>
>
> "/R-devel/lib64/R/library/human.db0/extdata/chipsrc_human.sqlite")
>
>
> dbGetQuery(con, "select count(*) from ensembl where ensid like
>
>
> 'ENSPTR%';")
> count(*)
> 1 16207
>
>
> dbGetQuery(con, "select count(*) from ensembl where ensid like
>
>
> 'ENSG%';")
> count(*)
> 1 28973
>
> On Mon, Apr 22, 2019 at 11:54 PM Aaron Lun <
> infinite.monkeys.with.keyboards using gmail.com<mailto:
> infinite.monkeys.with.keyboards using gmail.com>> wrote:
>
>
>
> Playing around with org.Hs.eg.db 3.8.0. What on earth is ENSPTRG0000...?
>
> > library(org.Hs.eg.db)
> > mapIds(org.Hs.eg.db, key="GCG", keytype="SYMBOL", column="ENSEMBL")
> 'select()' returned 1:many mapping between keys and columns
> GCG
> "ENSPTRG00000000777"
>
> Well, at least it still recovers the right identifier... eventually.
>
> > select(org.Hs.eg.db, key="GCG", keytype="SYMBOL", columns="ENSEMBL")
> 'select()' returned 1:many mapping between keys and columns
> SYMBOL ENSEMBL
> 1 GCG ENSPTRG00000000777
> 2 GCG ENSG00000115263
>
> The SYMBOL->Entrez ID relational table seems to be okay:
>
> > Y <- toTable(org.Hs.egSYMBOL)
> > Y[which(Y[,2]=="GCG"),]
> gene_id symbol
> 2152 2641 GCG
>
> So the cause is the Ensembl->Entrez mappings:
>
> > Z <- toTable(org.Hs.egENSEMBL2EG)
> > Z[Z[,1]==2641,]
> gene_id ensembl_id
> 3028 2641 ENSPTRG00000000777
> 3029 2641 ENSG00000115263
>
> Googling suggests that ENSPTRG00000000777 is an identifier for some
> other gene in one of the other monkeys. Hardly "Hs" stuff.
>
> Session info (not technically R 3.6, but I didn't think that would have
> been the cause):
>
>
>
> R Under development (unstable) (2019-04-11 r76379)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 18.04.2 LTS
>
> Matrix products: default
> BLAS: /home/luna/Software/R/trunk/lib/libRblas.so
> LAPACK: /home/luna/Software/R/trunk/lib/libRlapack.so
>
> 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=en_US.UTF-8 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] parallel stats4 stats graphics grDevices utils
>
>
> datasets
>
>
> [8] methods base
>
> other attached packages:
> [1] org.Hs.eg.db_3.8.0 AnnotationDbi_1.45.1 IRanges_2.17.5
> [4] S4Vectors_0.21.23 Biobase_2.43.1 BiocGenerics_0.29.2
>
> loaded via a namespace (and not attached):
> [1] Rcpp_1.0.1 digest_0.6.18 DBI_1.0.0 RSQLite_2.1.1
> [5] blob_1.1.1 bit64_0.9-7 bit_1.1-14 compiler_3.7.0
> [9] pkgconfig_2.0.2 memoise_1.1.0
>
>
>
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> --
> James W. MacDonald, M.S.
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>
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