How to make a db package for Agilent-015354 Bovine Oligo Microarray (4x44K)?
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Dear whom it may concern, I try to find out the way to make a db package for Agilent-015354 Bovine Oligo Microarray (4x44K). Since I'm very new to Bioinformatics and R, would you please prove/guide me step by step? These are what I plan to do. 1. I plan to make a table with two column containing with ProbeID and Target GeneID with no header. 2. I make a db package with makeDBPackage function as indicated in "Creating a New Annotation Package using SQLForge". I plan to write script exactly the same but have no idea which dbschemas to use; BOVINE_DB or BOVINECHIP_DB. Please help me prove these steps. Best Regards, Kaj -- output of sessionInfo(): sessionInfo() -- Sent via the guest posting facility at bioconductor.org.
Microarray Annotation oligo Microarray Annotation oligo • 848 views
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@kaj-chokeshaiusaha-5769
Last seen 8.1 years ago
Dear all, I've tried the script as following.. library(AnnotationForge) bov_9712<-read.table("A-GEOD-9712.adf.txt", skip=13, sep = "\t", header = FALSE, as.is = TRUE, fill=T)[,c(2,5)] #Here at this step bov_9712 contained with 2 column data : Spot_ID and Genebank# output="D:/Progect for MOU/Detailed Projects/Cumulus cell/Cow GPL9712" makeDBPackage("BOVINECHIP_DB", affy=FALSE, prefix="bov", fileName=bov_9712, baseMapType="gb", outputDir=output, version="1.0.0", manufacturer = "Agilent Technologies", chipName = "Agilent-015354 Bovine Oligo Microarray") then R show me.. Error in read.table(file = file, header = header, sep = sep, quote = quote, : 'file' must be a character string or connection I also try using BOVINE_DB in 'makeDBPackage'. It show me no error but doesn't give me back any file Please suggest me, Kaj On Sun, Feb 17, 2013 at 7:07 PM, Kaj Chokeshaiusaha [guest] < guest@bioconductor.org> wrote: > > Dear whom it may concern, > > I try to find out the way to make a db package for Agilent-015354 Bovine > Oligo Microarray (4x44K). Since I'm very new to Bioinformatics and R, would > you please prove/guide me step by step? > These are what I plan to do. > > 1. I plan to make a table with two column containing with ProbeID and > Target GeneID with no header. > 2. I make a db package with makeDBPackage function as indicated in > "Creating a New Annotation Package using > SQLForge". I plan to write script exactly the same but have no idea which > dbschemas to use; BOVINE_DB or BOVINECHIP_DB. > > Please help me prove these steps. > Best Regards, > Kaj > > > -- output of sessionInfo(): > > sessionInfo() > > -- > Sent via the guest posting facility at bioconductor.org. > [[alternative HTML version deleted]]
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Hi Kaj, That error means that your fileName parameter needs to be passed as a string. If you instead pass bov_9712 as you have below (with no quotes), R will think that you mean to pass an object that is called bov_9712, (instead of the string "bov_9712") and when it gets to the point where it is ready to try and actually read that file name into R, it will give you the error below. Please let me know if you still have questions. Marc On 02/18/2013 11:09 PM, Kaj Chokeshaiusaha wrote: > Dear all, > > I've tried the script as following.. > > library(AnnotationForge) > > bov_9712<-read.table("A-GEOD-9712.adf.txt", skip=13, sep = "\t", > header = FALSE, as.is = TRUE, fill=T)[,c(2,5)] > > #Here at this step bov_9712 contained with 2 column data : Spot_ID and > Genebank# > > output="D:/Progect for MOU/Detailed Projects/Cumulus cell/Cow GPL9712" > > makeDBPackage("BOVINECHIP_DB", > affy=FALSE, > prefix="bov", > fileName=bov_9712, > baseMapType="gb", > outputDir=output, > version="1.0.0", > manufacturer = "Agilent Technologies", > chipName = "Agilent-015354 Bovine Oligo Microarray") > > then R show me.. > > Error in read.table(file = file, header = header, sep = sep, quote = quote, > : > 'file' must be a character string or connection > > I also try using BOVINE_DB in 'makeDBPackage'. It show me no error but > doesn't give me back any file > > Please suggest me, > Kaj > > On Sun, Feb 17, 2013 at 7:07 PM, Kaj Chokeshaiusaha [guest] < > guest at bioconductor.org> wrote: > >> Dear whom it may concern, >> >> I try to find out the way to make a db package for Agilent-015354 Bovine >> Oligo Microarray (4x44K). Since I'm very new to Bioinformatics and R, would >> you please prove/guide me step by step? >> These are what I plan to do. >> >> 1. I plan to make a table with two column containing with ProbeID and >> Target GeneID with no header. >> 2. I make a db package with makeDBPackage function as indicated in >> "Creating a New Annotation Package using >> SQLForge". I plan to write script exactly the same but have no idea which >> dbschemas to use; BOVINE_DB or BOVINECHIP_DB. >> >> Please help me prove these steps. >> Best Regards, >> Kaj >> >> >> -- output of sessionInfo(): >> >> sessionInfo() >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> > [[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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Hi Kaj, That error means that you have previously tried to make this package (and presumably failed or you wouldn't be trying again). I am guessing that this is probably from when you were passing in the wrong argument type (from when you wrote in before). So what is wrong now is that the old half finished .sqlite file is still in your working directory (which is why there is a metadata table there already). Please delete all files that were generated from when you did this before, and start again. Marc Dear R helpers, I try to to create .db for Bovine Agilent Microarray Ship. R shows me error as indicated >/ library(AnnotationForge) />/ setwd("D:\\Progect for MOU\\Detailed Projects\\Cumulus cell") />/ bov_9712<-read.table("015354_D_GeneList_20061130.txt", sep = "\t", skip=1, /+ header = FALSE, as.is = TRUE, fill=T)[,c(1,5)] >/ write.table(bov_9712, file = "bov_9712.txt", sep = "\t", /+ row.names=F, col.names=F) >/ output="D:\\Progect for MOU\\Detailed Projects\\Cumulus cell\\Annotations" />/ makeDBPackage("BOVINECHIP_DB", /+ affy=FALSE, + prefix="bov_9712gbNRef", + fileName="bov_9712.txt", + baseMapType="gbNRef", + outputDir=output, + version="1.0.0", + manufacturer = "Agilent Technologies", + chipName = "Agilent-015354 Bovine Oligo Microarray") Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: table metadata already exists) Please describe what does the error indicate? and please guide me how to solve it. Best Regards, Kaj -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Thai_Thailand.874 LC_CTYPE=Thai_Thailand.874 [3] LC_MONETARY=Thai_Thailand.874 LC_NUMERIC=C [5] LC_TIME=Thai_Thailand.874 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.8.3 AnnotationForge_1.0.3 org.Hs.eg.db_2.8.0 [4] RSQLite_0.11.2 DBI_0.2-5 AnnotationDbi_1.20.3 [7] Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] IRanges_1.16.5 parallel_2.15.1 stats4_2.15.1 tools_2.15.1 -- Sent via the guest posting facility at bioconductor.org. [[alternative HTML version deleted]]
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