[Bioc-devel] Weird monkey identifiers in org.Hs.eg.db

Sat Apr 27 00:41:00 CEST 2019

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

_______________________________________________
Bioc-devel using r-project.org<mailto:Bioc-devel using r-project.org> mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=pRzAhoukTjoi6JCrxpZEHER0Dj7wqeCghzULGLFaTNQ&s=MxM9vCqiDsqvIw8l3iyam0_WN-7LHwlr6YiG_zb4vkQ&e=

--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel using r-project.org<mailto:Bioc-devel using r-project.org> mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=pRzAhoukTjoi6JCrxpZEHER0Dj7wqeCghzULGLFaTNQ&s=MxM9vCqiDsqvIw8l3iyam0_WN-7LHwlr6YiG_zb4vkQ&e=

This email message may contain legally privileged and/or confidential
information.  If you are not the intended recipient(s), or the employee or
agent responsible for the delivery of this message to the intended
recipient(s), you are hereby notified that any disclosure, copying,
distribution, or use of this email message is prohibited.  If you have
received this message in error, please notify the sender immediately by
e-mail and delete this email message from your computer. Thank you.
        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel using r-project.org<mailto:Bioc-devel using r-project.org> mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=pRzAhoukTjoi6JCrxpZEHER0Dj7wqeCghzULGLFaTNQ&s=MxM9vCqiDsqvIw8l3iyam0_WN-7LHwlr6YiG_zb4vkQ&e=

The information in this e-mail is intended only for th...{{dropped:15}}

_______________________________________________
Bioc-devel using r-project.org<mailto:Bioc-devel using r-project.org> mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=pRzAhoukTjoi6JCrxpZEHER0Dj7wqeCghzULGLFaTNQ&s=MxM9vCqiDsqvIw8l3iyam0_WN-7LHwlr6YiG_zb4vkQ&e=

--
Herv� Pag�s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages using fredhutch.org<mailto:hpages using fredhutch.org>
Phone:  (206) 667-5791
Fax:    (206) 667-1319

        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel using r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
	[[alternative HTML version deleted]]