Error using makeDBPackage() from AnnotationForge package
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gabriel teku ▴ 80
@gabriel-teku-4427
Last seen 6.7 years ago
Sweden
Hi bioc, I'm having trouble with the problem of creating the annotation package for organism = human, array type = custom array, and I it'll really be nice to get some help at this point. Here is what I've done so far without success: -- I've followed the instructions given in the AnnotationForge package vignettes titled "SQLForge: An easy way to create a new annotation package with a standard database schema." -- First, I created the probe --> entrezgene id mapping for the custom array -- Re-installed the org.Hs.eg.db package -- Run the makeDBPackage function, which fails Here is the code snippet > head(hcg3278_ID) # table of probe --> entrez id mapping probe_id entregene_id 1 19249_1 153579 2 19251_1 53335 3 19253_1 3603 4 19255_1 6004 5 19257_1 115350 6 23809_1 729082> write.table(hcg3278_ID, file="hcg3278_ID", sep="\t", row=F, col=F) > makeDBPackage(schema = "HUMANCHIP_DB", affy=F, pref="hcg3278", fileName="hcg3278_ID", baseMapType="eg", version="1.0.0", manufacturer="The Staudt laboratory", chipName="NCI/Staudt human 15K v13", outputDir = getwd()) baseMapType is eg Prepending MetadataCreating Genes tableError in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (RS_SQLite_exec: could not execute1: genes.gene_id may not be NULL) > sessionInfo()R version 3.0.1 (2013-05-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] AnnotationForge_1.2.2 org.Hs.eg.db_2.9.0 RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.22.6 Biobase_2.20.1 [7] BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] data.table_1.8.10 IRanges_1.18.3 plyr_1.8 stats4_3.0.1 tools_3.0.1 Thanks in advance Gabriel Teku [[alternative HTML version deleted]]
Annotation probe AnnotationForge Annotation probe AnnotationForge • 1.1k views
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 5.8 years ago
United States
Hi Gabriel, I am confused about why you are posting this? Did you not see Jims response yesterday? The one in which he responded to having already responded to the identical question posted earlier? I feel sudden concern that we have somehow gotten stuck in some sort of recursive mailing list question... ;) Here is where it stood as of yesterday: https://stat.ethz.ch/pipermail/bioconductor/2013-September/054891.html If it's really important that you use your own file, could you please send it to me so that I can have a look at it? Marc On 09/13/2013 04:06 AM, Gabriel Teku wrote: > Hi bioc, > I'm having trouble with the problem of creating the annotation package for > organism = human, array type = custom array, and I it'll really be nice to > get some help at this point. > Here is what I've done so far without success: > -- I've followed the instructions given in the AnnotationForge package > vignettes titled "SQLForge: An easy way to create a new annotation package > with a standard database schema." > -- First, I created the probe --> entrezgene id mapping for the custom > array > -- Re-installed the org.Hs.eg.db package > -- Run the makeDBPackage function, which fails > Here is the code snippet > >> head(hcg3278_ID) # table of probe --> entrez id mapping probe_id entregene_id > 1 19249_1 153579 > 2 19251_1 53335 > 3 19253_1 3603 > 4 19255_1 6004 > 5 19257_1 115350 > 6 23809_1 729082> write.table(hcg3278_ID, file="hcg3278_ID", > sep="\t", row=F, col=F) > >> makeDBPackage(schema = "HUMANCHIP_DB", affy=F, pref="hcg3278", fileName="hcg3278_ID", baseMapType="eg", version="1.0.0", manufacturer="The Staudt laboratory", chipName="NCI/Staudt human 15K v13", outputDir = getwd()) > baseMapType is eg > Prepending MetadataCreating Genes tableError in > sqliteExecStatement(con, statement, bind.data) : > RS-DBI driver: (RS_SQLite_exec: could not execute1: genes.gene_id > may not be NULL) > > >> sessionInfo()R version 3.0.1 (2013-05-16) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > LC_MONETARY=en_US.UTF-8 > [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C > LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] AnnotationForge_1.2.2 org.Hs.eg.db_2.9.0 RSQLite_0.11.4 > DBI_0.2-7 AnnotationDbi_1.22.6 Biobase_2.20.1 > [7] BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] data.table_1.8.10 IRanges_1.18.3 plyr_1.8 stats4_3.0.1 > tools_3.0.1 > > > Thanks in advance > > > Gabriel Teku > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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