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.vantw...@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-boun...@r-project.org> on behalf of Pages, > Herve <hpa...@fredhutch.org> > *Sent:* Thursday, April 25, 2019 9:19:35 PM > *To:* Aaron Lun; Vincent Carey > *Cc:* Bioc-devel; jmac...@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 <st...@channing.harvard.edu > ><mailto:st...@channing.harvard.edu> > wrote: > > > > Has this situation been rectified? > > On Tue, Apr 23, 2019 at 11:40 AM Van Twisk, Daniel < > daniel.vantw...@roswellpark.org<mailto:daniel.vantw...@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-boun...@r-project.org><mailto: > bioc-devel-boun...@r-project.org> on behalf of James > W. MacDonald <jmac...@uw.edu><mailto:jmac...@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.keyboa...@gmail.com<mailto: > infinite.monkeys.with.keyboa...@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@r-project.org<mailto:Bioc-devel@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@r-project.org<mailto:Bioc-devel@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. 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Thank you. > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org<mailto:Bioc-devel@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@r-project.org<mailto:Bioc-devel@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= > > > -- > Hervé Pagès > > 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: hpa...@fredhutch.org<mailto:hpa...@fredhutch.org> > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@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. 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