Re: [Bioc-devel] Weird monkey identifiers in org.Hs.eg.db
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 on behalf of Pages, > Herve > *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 ><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> on behalf of James > W. MacDonald <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(*) > 116207 > > > dbGetQuery(con, "select count(*) from ensembl where ensid like > > > 'ENSG%';") > count(*) > 128973 > > On Mon, Apr 22, 2019 at 11:54 PM Aaron Lun < > infinite.monkeys.with.keyboa...@gmail.com infinite.monkeys.with.keyboa...@gmail.com>> wrote: > > > > Playing around with org.Hs.eg.db 3.8.0. What on earth is ENSPTRG...? > > > 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 > "ENSPTRG777" > > 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 >SYMBOLENSEMBL > 1GCG ENSPTRG777 > 2GCGENSG0115263 > > The SYMBOL->Entrez ID relational table seems to be okay: > > > Y <- toTable(org.Hs.egSYMBOL) > > Y[which(Y[,2]=="GCG"),] > gene_id symbol > 21522641GCG > > So the cause is the Ensembl->Entrez mappings: > > > Z <- toTable(org.Hs.egENSEMBL2EG) > > Z[Z[,1]==2641,] > gene_id ensembl_id > 30282641 ENSPTRG777 > 30292641ENSG0115263 > > Googling suggests that ENSPTRG777 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-8LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRES
Re: [Bioc-devel] Weird monkey identifiers in org.Hs.eg.db
I've pushed new 3.8.2 orgdbs that should propagate soon. They do not have this issue. From: Bioc-devel on behalf of Pages, Herve 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 <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 <mailto:bioc-devel-boun...@r-project.org> on behalf of James W. MacDonald <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(*) 116207 dbGetQuery(con, "select count(*) from ensembl where ensid like 'ENSG%';") count(*) 128973 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 ENSPTRG...? > 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 "ENSPTRG777" 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 SYMBOLENSEMBL 1GCG ENSPTRG777 2GCGENSG0115263 The SYMBOL->Entrez ID relational table seems to be okay: > Y <- toTable(org.Hs.egSYMBOL) > Y[which(Y[,2]=="GCG"),] gene_id symbol 21522641GCG So the cause is the Ensembl->Entrez mappings: > Z <- toTable(org.Hs.egENSEMBL2EG) > Z[Z[,1]==2641,] gene_id ensembl_id 30282641 ENSPTRG777 30292641ENSG0115263 Googling suggests that ENSPTRG777 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-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_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 stats4stats 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_0.21.23Biobase_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=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=pRzAhoukTjoi6JCrxpZE
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 <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 <mailto:bioc-devel-boun...@r-project.org> on behalf of James W. MacDonald <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(*) 116207 dbGetQuery(con, "select count(*) from ensembl where ensid like 'ENSG%';") count(*) 128973 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 ENSPTRG...? > 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 "ENSPTRG777" 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 SYMBOLENSEMBL 1GCG ENSPTRG777 2GCGENSG0115263 The SYMBOL->Entrez ID relational table seems to be okay: > Y <- toTable(org.Hs.egSYMBOL) > Y[which(Y[,2]=="GCG"),] gene_id symbol 21522641GCG So the cause is the Ensembl->Entrez mappings: > Z <- toTable(org.Hs.egENSEMBL2EG) > Z[Z[,1]==2641,] gene_id ensembl_id 30282641 ENSPTRG777 30292641ENSG0115263 Googling suggests that ENSPTRG777 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-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_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 stats4stats 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_0.21.23Biobase_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=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=pRzAhoukTjoi6JCrxpZEHER0Dj7wqeCghzULGLFaTNQ=MxM9vCqiDsqvIw8l3iyam0_WN-7LHwlr6YiG_zb4vkQ= -- 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]]
Re: [Bioc-devel] Weird monkey identifiers in org.Hs.eg.db
Has this situation been rectified? On Tue, Apr 23, 2019 at 11:40 AM Van Twisk, Daniel < 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 on behalf of James W. > MacDonald > 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(*) > 116207 > > dbGetQuery(con, "select count(*) from ensembl where ensid like 'ENSG%';") > count(*) > 128973 > > On Mon, Apr 22, 2019 at 11:54 PM Aaron Lun < > infinite.monkeys.with.keyboa...@gmail.com> wrote: > > > Playing around with org.Hs.eg.db 3.8.0. What on earth is ENSPTRG...? > > > > > 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 > > "ENSPTRG777" > > > > 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 > >SYMBOLENSEMBL > > 1GCG ENSPTRG777 > > 2GCGENSG0115263 > > > > The SYMBOL->Entrez ID relational table seems to be okay: > > > > > Y <- toTable(org.Hs.egSYMBOL) > > > Y[which(Y[,2]=="GCG"),] > > gene_id symbol > > 21522641GCG > > > > So the cause is the Ensembl->Entrez mappings: > > > > > Z <- toTable(org.Hs.egENSEMBL2EG) > > > Z[Z[,1]==2641,] > > gene_id ensembl_id > > 30282641 ENSPTRG777 > > 30292641ENSG0115263 > > > > Googling suggests that ENSPTRG777 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-8LC_COLLATE=en_US.UTF-8 > > > [5] LC_MONETARY=en_US.UTF-8LC_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 stats4stats 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_0.21.23Biobase_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 mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > -- > 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 mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > This email message may contain legally pr
Re: [Bioc-devel] Weird monkey identifiers in org.Hs.eg.db
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 on behalf of James W. MacDonald 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(*) 116207 > dbGetQuery(con, "select count(*) from ensembl where ensid like 'ENSG%';") count(*) 128973 On Mon, Apr 22, 2019 at 11:54 PM Aaron Lun < infinite.monkeys.with.keyboa...@gmail.com> wrote: > Playing around with org.Hs.eg.db 3.8.0. What on earth is ENSPTRG...? > > > 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 > "ENSPTRG777" > > 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 >SYMBOLENSEMBL > 1GCG ENSPTRG777 > 2GCGENSG0115263 > > The SYMBOL->Entrez ID relational table seems to be okay: > > > Y <- toTable(org.Hs.egSYMBOL) > > Y[which(Y[,2]=="GCG"),] > gene_id symbol > 21522641GCG > > So the cause is the Ensembl->Entrez mappings: > > > Z <- toTable(org.Hs.egENSEMBL2EG) > > Z[Z[,1]==2641,] > gene_id ensembl_id > 30282641 ENSPTRG777 > 30292641ENSG0115263 > > Googling suggests that ENSPTRG777 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-8LC_COLLATE=en_US.UTF-8 > > [5] LC_MONETARY=en_US.UTF-8LC_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 stats4stats 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_0.21.23Biobase_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 mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- 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 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]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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(*) 116207 > dbGetQuery(con, "select count(*) from ensembl where ensid like 'ENSG%';") count(*) 128973 On Mon, Apr 22, 2019 at 11:54 PM Aaron Lun < infinite.monkeys.with.keyboa...@gmail.com> wrote: > Playing around with org.Hs.eg.db 3.8.0. What on earth is ENSPTRG...? > > > 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 > "ENSPTRG777" > > 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 >SYMBOLENSEMBL > 1GCG ENSPTRG777 > 2GCGENSG0115263 > > The SYMBOL->Entrez ID relational table seems to be okay: > > > Y <- toTable(org.Hs.egSYMBOL) > > Y[which(Y[,2]=="GCG"),] > gene_id symbol > 21522641GCG > > So the cause is the Ensembl->Entrez mappings: > > > Z <- toTable(org.Hs.egENSEMBL2EG) > > Z[Z[,1]==2641,] > gene_id ensembl_id > 30282641 ENSPTRG777 > 30292641ENSG0115263 > > Googling suggests that ENSPTRG777 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-8LC_COLLATE=en_US.UTF-8 > > [5] LC_MONETARY=en_US.UTF-8LC_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 stats4stats 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_0.21.23Biobase_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 mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- 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 mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Weird monkey identifiers in org.Hs.eg.db
Playing around with org.Hs.eg.db 3.8.0. What on earth is ENSPTRG...? > 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 "ENSPTRG777" 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 SYMBOLENSEMBL 1GCG ENSPTRG777 2GCGENSG0115263 The SYMBOL->Entrez ID relational table seems to be okay: > Y <- toTable(org.Hs.egSYMBOL) > Y[which(Y[,2]=="GCG"),] gene_id symbol 21522641GCG So the cause is the Ensembl->Entrez mappings: > Z <- toTable(org.Hs.egENSEMBL2EG) > Z[Z[,1]==2641,] gene_id ensembl_id 30282641 ENSPTRG777 30292641ENSG0115263 Googling suggests that ENSPTRG777 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-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_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 stats4stats 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_0.21.23Biobase_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 mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
