Question: newbie problems with AnnBuilder
0
gravatar for Mark W Kimpel
10.9 years ago by
Mark W Kimpel830
Mark W Kimpel830 wrote:
I'm having problems getting AnnBuilder to work with the Affy Rat Gene ST array data supplied by Affy. Using the code chunk below, I am able to get AnnBuilder to create the annotation object, but it crashes, I believe, when it tries to save it. I should also mention that I had a previous crash when I had a madecdfenv package directory in place that used the same name. I got a "file lock" error, so I temporarily renamed the directory to see if this fixed the problem. As below, the error changed, but I still can't get the script to work. I suspect that there is a fundamental misunderstaning on my part related to how the annotation package should relate to the cdf package or some naming convention related to one or both. Mark > require(AnnBuilder); require(makecdfenv) > myBase <- "RaGene-1_0-st-v1.na26.rn4.transcript.probe- entrez_gene.csv" > myBaseType <- "ll" > mySrcUrls <- getSrcUrl("all", "Rattus norvegicus") > > ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = + myBaseType, pkgName = substring(cleancdfname("RaGene-1_0-st-v1"), + 1, (nchar(cleancdfname("RaGene-1_0-st-v1")) - 3)), + pkgPath = '~/R_HOME/site-library-2.8.0', organism = "Rattus norvegicus", version = "1.0", + author = list(authors = "Mark W Kimpel", maintainer = + "mkimpel@iupui.edu"), fromWeb = TRUE) Read 1 item Read 1 item [1] "4450 2 2" Error in lazyLoadDBinsertValue(data, datafile, ascii, compress, envhook) : cannot open file '~/R_HOME/site-library-2.8.0/ragene10stv1/data/Rdata.rdb': No such file or directory Enter a frame number, or 0 to exit 1: ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = myBaseTy 2: makeLLDB(file.path(pkgPath, pkgName), compress = TRUE) 3: tools:::makeLazyLoadDB(dataEnv, dbbase, compress = compress) 4: lazyLoadDBinsertVariable(vars[i], from, datafile, ascii, compress, envhook) 5: function (e) 6: lazyLoadDBinsertValue(data, datafile, ascii, compress, envhook) Selection: 1 Browse[1]> annotation[1:2,] ENTREZID PROBE ACCNUM GO [1,] "100008565" "10766774" NA NA [2,] "100034253" "10937540" NA "GO:0005525@IEA;GO:0005622@IEA" PMID SYMBOL [1,] "16804107;17292978" "Slc39a4l" [2,] "8889548" "Gnl3l" GENENAME CHR [1,] "solute carrier family 39 (zinc transporter), member 4-like" NA [2,] "guanine nucleotide binding protein-like 3 (nucleolar)-like" "X" MAP REFSEQ UNIGENE CHRLOC PATH [1,] NA "NM_001101021;NP_001094491" "Rn.10120" "NA" NA [2,] "Xq14-q21" "NM_001081958;NP_001075427" "Rn.164274" "-40301218@X" NA ENZYME PFAM PROSITE [1,] NA "NA@IPI00817057" "NA@IPI00817057" [2,] NA "PF01926@IPI00362844" "NA@IPI00362844" ------------------------------------------------------------ Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 399-1219 Home Skype: mkimpel "The real problem is not whether machines think but whether men do." -- B. F. Skinner ****************************************************************** [[alternative HTML version deleted]]
ADD COMMENTlink modified 10.9 years ago by Marc Carlson7.2k • written 10.9 years ago by Mark W Kimpel830
Answer: newbie problems with AnnBuilder
0
gravatar for Marc Carlson
10.9 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Hi Mark, AnnBuilder is on its way out. Please have a look at the SQLforge.pdf vignette which can be found here: http://www.bioconductor.org/packages/2.3/bioc/html/AnnotationDbi.html If you have further questions after reading this, then please just ask, and we should be able to help you out. Marc Mark Kimpel wrote: > I'm having problems getting AnnBuilder to work with the Affy Rat Gene ST > array data supplied by Affy. Using the code chunk below, I am able to get > AnnBuilder to create the annotation object, but it crashes, I believe, when > it tries to save it. I should also mention that I had a previous crash when > I had a madecdfenv package directory in place that used the same name. I got > a "file lock" error, so I temporarily renamed the directory to see if this > fixed the problem. As below, the error changed, but I still can't get the > script to work. > > I suspect that there is a fundamental misunderstaning on my part related to > how the annotation package should relate to the cdf package or some naming > convention related to one or both. > > Mark > > >> require(AnnBuilder); require(makecdfenv) >> myBase <- "RaGene-1_0-st-v1.na26.rn4.transcript.probe- entrez_gene.csv" >> myBaseType <- "ll" >> mySrcUrls <- getSrcUrl("all", "Rattus norvegicus") >> >> ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = >> > + myBaseType, pkgName = > substring(cleancdfname("RaGene-1_0-st-v1"), > + 1, (nchar(cleancdfname("RaGene- 1_0-st-v1")) - 3)), > + pkgPath = '~/R_HOME/site-library-2.8.0', organism = "Rattus > norvegicus", version = "1.0", > + author = list(authors = "Mark W Kimpel", maintainer = > + "mkimpel at iupui.edu"), fromWeb = TRUE) > Read 1 item > Read 1 item > [1] "4450 2 2" > Error in lazyLoadDBinsertValue(data, datafile, ascii, compress, envhook) : > cannot open file > '~/R_HOME/site-library-2.8.0/ragene10stv1/data/Rdata.rdb': No such file or > directory > > Enter a frame number, or 0 to exit > > 1: ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = > myBaseTy > 2: makeLLDB(file.path(pkgPath, pkgName), compress = TRUE) > 3: tools:::makeLazyLoadDB(dataEnv, dbbase, compress = compress) > 4: lazyLoadDBinsertVariable(vars[i], from, datafile, ascii, compress, > envhook) > 5: function (e) > 6: lazyLoadDBinsertValue(data, datafile, ascii, compress, envhook) > > Selection: 1 > Browse[1]> annotation[1:2,] > ENTREZID PROBE ACCNUM GO > [1,] "100008565" "10766774" NA NA > [2,] "100034253" "10937540" NA "GO:0005525 at IEA;GO:0005622 at IEA" > PMID SYMBOL > [1,] "16804107;17292978" "Slc39a4l" > [2,] "8889548" "Gnl3l" > GENENAME CHR > [1,] "solute carrier family 39 (zinc transporter), member 4-like" NA > [2,] "guanine nucleotide binding protein-like 3 (nucleolar)-like" "X" > MAP REFSEQ UNIGENE CHRLOC PATH > [1,] NA "NM_001101021;NP_001094491" "Rn.10120" "NA" NA > [2,] "Xq14-q21" "NM_001081958;NP_001075427" "Rn.164274" "-40301218 at X" NA > ENZYME PFAM PROSITE > [1,] NA "NA at IPI00817057" "NA at IPI00817057" > [2,] NA "PF01926 at IPI00362844" "NA at IPI00362844" > ------------------------------------------------------------ > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > Indiana University School of Medicine > > 15032 Hunter Court, Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile & VoiceMail > (317) 399-1219 Home > Skype: mkimpel > > "The real problem is not whether machines think but whether men do." -- B. > F. Skinner > ****************************************************************** > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
ADD COMMENTlink written 10.9 years ago by Marc Carlson7.2k
Build with AnnotationDbi was uneventful, but I have been unable to install the package or use it as is. If the package is just placed in my site-library, I get: 'ragene10stv1.db' is not a valid package -- installed < 2.0.0? If I tar the package and try R CMD INSTALL, I get: cannot extract package from 'ragene10stv1.db.tar.gz' What approach should I be using? Mark ------------------------------------------------------------ Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 399-1219 Home Skype: mkimpel "The real problem is not whether machines think but whether men do." -- B. F. Skinner ****************************************************************** On Tue, Oct 21, 2008 at 6:41 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: > > Hi Mark, > > AnnBuilder is on its way out. Please have a look at the SQLforge.pdf > vignette which can be found here: > > http://www.bioconductor.org/packages/2.3/bioc/html/AnnotationDbi.html > > If you have further questions after reading this, then please just ask, > and we should be able to help you out. > > > Marc > > > > Mark Kimpel wrote: > > I'm having problems getting AnnBuilder to work with the Affy Rat Gene ST > > array data supplied by Affy. Using the code chunk below, I am able to get > > AnnBuilder to create the annotation object, but it crashes, I believe, when > > it tries to save it. I should also mention that I had a previous crash when > > I had a madecdfenv package directory in place that used the same name. I got > > a "file lock" error, so I temporarily renamed the directory to see if this > > fixed the problem. As below, the error changed, but I still can't get the > > script to work. > > > > I suspect that there is a fundamental misunderstaning on my part related to > > how the annotation package should relate to the cdf package or some naming > > convention related to one or both. > > > > Mark > > > > > >> require(AnnBuilder); require(makecdfenv) > >> myBase <- "RaGene-1_0-st-v1.na26.rn4.transcript.probe- entrez_gene.csv" > >> myBaseType <- "ll" > >> mySrcUrls <- getSrcUrl("all", "Rattus norvegicus") > >> > >> ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = > >> > > + myBaseType, pkgName = > > substring(cleancdfname("RaGene-1_0-st-v1"), > > + 1, (nchar(cleancdfname("RaGene- 1_0-st-v1")) - 3)), > > + pkgPath = '~/R_HOME/site-library-2.8.0', organism = "Rattus > > norvegicus", version = "1.0", > > + author = list(authors = "Mark W Kimpel", maintainer = > > + "mkimpel at iupui.edu"), fromWeb = TRUE) > > Read 1 item > > Read 1 item > > [1] "4450 2 2" > > Error in lazyLoadDBinsertValue(data, datafile, ascii, compress, envhook) : > > cannot open file > > '~/R_HOME/site-library-2.8.0/ragene10stv1/data/Rdata.rdb': No such file or > > directory > > > > Enter a frame number, or 0 to exit > > > > 1: ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = > > myBaseTy > > 2: makeLLDB(file.path(pkgPath, pkgName), compress = TRUE) > > 3: tools:::makeLazyLoadDB(dataEnv, dbbase, compress = compress) > > 4: lazyLoadDBinsertVariable(vars[i], from, datafile, ascii, compress, > > envhook) > > 5: function (e) > > 6: lazyLoadDBinsertValue(data, datafile, ascii, compress, envhook) > > > > Selection: 1 > > Browse[1]> annotation[1:2,] > > ENTREZID PROBE ACCNUM GO > > [1,] "100008565" "10766774" NA NA > > [2,] "100034253" "10937540" NA "GO:0005525 at IEA;GO:0005622 at IEA" > > PMID SYMBOL > > [1,] "16804107;17292978" "Slc39a4l" > > [2,] "8889548" "Gnl3l" > > GENENAME CHR > > [1,] "solute carrier family 39 (zinc transporter), member 4-like" NA > > [2,] "guanine nucleotide binding protein-like 3 (nucleolar)-like" "X" > > MAP REFSEQ UNIGENE CHRLOC PATH > > [1,] NA "NM_001101021;NP_001094491" "Rn.10120" "NA" NA > > [2,] "Xq14-q21" "NM_001081958;NP_001075427" "Rn.164274" "-40301218 at X" NA > > ENZYME PFAM PROSITE > > [1,] NA "NA at IPI00817057" "NA at IPI00817057" > > [2,] NA "PF01926 at IPI00362844" "NA at IPI00362844" > > ------------------------------------------------------------ > > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > > Indiana University School of Medicine > > > > 15032 Hunter Court, Westfield, IN 46074 > > > > (317) 490-5129 Work, & Mobile & VoiceMail > > (317) 399-1219 Home > > Skype: mkimpel > > > > "The real problem is not whether machines think but whether men do." -- B. > > F. Skinner > > ****************************************************************** > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > >
ADD REPLYlink written 10.9 years ago by Mark W Kimpel830
On Wed, Oct 22, 2008 at 11:07 AM, Mark Kimpel <mwkimpel at="" gmail.com=""> wrote: > Build with AnnotationDbi was uneventful, but I have been unable to > install the package or use it as is. > > If the package is just placed in my site-library, I get: > 'ragene10stv1.db' is not a valid package -- installed < 2.0.0? > > If I tar the package and try R CMD INSTALL, I get: > cannot extract package from 'ragene10stv1.db.tar.gz' > > What approach should I be using? You can just R CMD INSTALL ragene10stv1.db where ragene10stv1.db is the directory that contains the package (right above the DESCRIPTION file). Sean > On Tue, Oct 21, 2008 at 6:41 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: >> >> Hi Mark, >> >> AnnBuilder is on its way out. Please have a look at the SQLforge.pdf >> vignette which can be found here: >> >> http://www.bioconductor.org/packages/2.3/bioc/html/AnnotationDbi.html >> >> If you have further questions after reading this, then please just ask, >> and we should be able to help you out. >> >> >> Marc >> >> >> >> Mark Kimpel wrote: >> > I'm having problems getting AnnBuilder to work with the Affy Rat Gene ST >> > array data supplied by Affy. Using the code chunk below, I am able to get >> > AnnBuilder to create the annotation object, but it crashes, I believe, when >> > it tries to save it. I should also mention that I had a previous crash when >> > I had a madecdfenv package directory in place that used the same name. I got >> > a "file lock" error, so I temporarily renamed the directory to see if this >> > fixed the problem. As below, the error changed, but I still can't get the >> > script to work. >> > >> > I suspect that there is a fundamental misunderstaning on my part related to >> > how the annotation package should relate to the cdf package or some naming >> > convention related to one or both. >> > >> > Mark >> > >> > >> >> require(AnnBuilder); require(makecdfenv) >> >> myBase <- "RaGene-1_0-st-v1.na26.rn4.transcript.probe- entrez_gene.csv" >> >> myBaseType <- "ll" >> >> mySrcUrls <- getSrcUrl("all", "Rattus norvegicus") >> >> >> >> ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = >> >> >> > + myBaseType, pkgName = >> > substring(cleancdfname("RaGene-1_0-st-v1"), >> > + 1, (nchar(cleancdfname("RaGene- 1_0-st-v1")) - 3)), >> > + pkgPath = '~/R_HOME/site-library-2.8.0', organism = "Rattus >> > norvegicus", version = "1.0", >> > + author = list(authors = "Mark W Kimpel", maintainer = >> > + "mkimpel at iupui.edu"), fromWeb = TRUE) >> > Read 1 item >> > Read 1 item >> > [1] "4450 2 2" >> > Error in lazyLoadDBinsertValue(data, datafile, ascii, compress, envhook) : >> > cannot open file >> > '~/R_HOME/site-library-2.8.0/ragene10stv1/data/Rdata.rdb': No such file or >> > directory >> > >> > Enter a frame number, or 0 to exit >> > >> > 1: ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = >> > myBaseTy >> > 2: makeLLDB(file.path(pkgPath, pkgName), compress = TRUE) >> > 3: tools:::makeLazyLoadDB(dataEnv, dbbase, compress = compress) >> > 4: lazyLoadDBinsertVariable(vars[i], from, datafile, ascii, compress, >> > envhook) >> > 5: function (e) >> > 6: lazyLoadDBinsertValue(data, datafile, ascii, compress, envhook) >> > >> > Selection: 1 >> > Browse[1]> annotation[1:2,] >> > ENTREZID PROBE ACCNUM GO >> > [1,] "100008565" "10766774" NA NA >> > [2,] "100034253" "10937540" NA "GO:0005525 at IEA;GO:0005622 at IEA" >> > PMID SYMBOL >> > [1,] "16804107;17292978" "Slc39a4l" >> > [2,] "8889548" "Gnl3l" >> > GENENAME CHR >> > [1,] "solute carrier family 39 (zinc transporter), member 4-like" NA >> > [2,] "guanine nucleotide binding protein-like 3 (nucleolar)-like" "X" >> > MAP REFSEQ UNIGENE CHRLOC PATH >> > [1,] NA "NM_001101021;NP_001094491" "Rn.10120" "NA" NA >> > [2,] "Xq14-q21" "NM_001081958;NP_001075427" "Rn.164274" "-40301218 at X" NA >> > ENZYME PFAM PROSITE >> > [1,] NA "NA at IPI00817057" "NA at IPI00817057" >> > [2,] NA "PF01926 at IPI00362844" "NA at IPI00362844" >> > ------------------------------------------------------------ >> > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >> > Indiana University School of Medicine >> > >> > 15032 Hunter Court, Westfield, IN 46074 >> > >> > (317) 490-5129 Work, & Mobile & VoiceMail >> > (317) 399-1219 Home >> > Skype: mkimpel >> > >> > "The real problem is not whether machines think but whether men do." -- B. >> > F. Skinner >> > ****************************************************************** >> > >> > [[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at stat.math.ethz.ch >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> > >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 10.9 years ago by Sean Davis21k
Interesting, it works from a command line outside of R, but when I had tried R> system('R CMD INSTALL ragene10stv1.db') I received an error message. I have used this approach successfully with other packages to avoid leaving R and starting a shell, but with this package I get: '* Installing to library '/home/mkimpel/R_HOME/site-library-2.8.0' ERROR: no packages specified' Well, thanks, it now is installed. Any comment on why my system() approach might not have worked? Mark ------------------------------------------------------------ Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 399-1219 Home Skype: mkimpel "The real problem is not whether machines think but whether men do." -- B. F. Skinner ****************************************************************** On Wed, Oct 22, 2008 at 11:53 AM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Wed, Oct 22, 2008 at 11:07 AM, Mark Kimpel <mwkimpel at="" gmail.com=""> wrote: >> Build with AnnotationDbi was uneventful, but I have been unable to >> install the package or use it as is. >> >> If the package is just placed in my site-library, I get: >> 'ragene10stv1.db' is not a valid package -- installed < 2.0.0? >> >> If I tar the package and try R CMD INSTALL, I get: >> cannot extract package from 'ragene10stv1.db.tar.gz' >> >> What approach should I be using? > > You can just > > R CMD INSTALL ragene10stv1.db > > where ragene10stv1.db is the directory that contains the package > (right above the DESCRIPTION file). > > Sean > > >> On Tue, Oct 21, 2008 at 6:41 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: >>> >>> Hi Mark, >>> >>> AnnBuilder is on its way out. Please have a look at the SQLforge.pdf >>> vignette which can be found here: >>> >>> http://www.bioconductor.org/packages/2.3/bioc/html/AnnotationDbi.html >>> >>> If you have further questions after reading this, then please just ask, >>> and we should be able to help you out. >>> >>> >>> Marc >>> >>> >>> >>> Mark Kimpel wrote: >>> > I'm having problems getting AnnBuilder to work with the Affy Rat Gene ST >>> > array data supplied by Affy. Using the code chunk below, I am able to get >>> > AnnBuilder to create the annotation object, but it crashes, I believe, when >>> > it tries to save it. I should also mention that I had a previous crash when >>> > I had a madecdfenv package directory in place that used the same name. I got >>> > a "file lock" error, so I temporarily renamed the directory to see if this >>> > fixed the problem. As below, the error changed, but I still can't get the >>> > script to work. >>> > >>> > I suspect that there is a fundamental misunderstaning on my part related to >>> > how the annotation package should relate to the cdf package or some naming >>> > convention related to one or both. >>> > >>> > Mark >>> > >>> > >>> >> require(AnnBuilder); require(makecdfenv) >>> >> myBase <- "RaGene-1_0-st-v1.na26.rn4.transcript.probe- entrez_gene.csv" >>> >> myBaseType <- "ll" >>> >> mySrcUrls <- getSrcUrl("all", "Rattus norvegicus") >>> >> >>> >> ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = >>> >> >>> > + myBaseType, pkgName = >>> > substring(cleancdfname("RaGene-1_0-st-v1"), >>> > + 1, (nchar(cleancdfname("RaGene- 1_0-st-v1")) - 3)), >>> > + pkgPath = '~/R_HOME/site-library-2.8.0', organism = "Rattus >>> > norvegicus", version = "1.0", >>> > + author = list(authors = "Mark W Kimpel", maintainer = >>> > + "mkimpel at iupui.edu"), fromWeb = TRUE) >>> > Read 1 item >>> > Read 1 item >>> > [1] "4450 2 2" >>> > Error in lazyLoadDBinsertValue(data, datafile, ascii, compress, envhook) : >>> > cannot open file >>> > '~/R_HOME/site-library-2.8.0/ragene10stv1/data/Rdata.rdb': No such file or >>> > directory >>> > >>> > Enter a frame number, or 0 to exit >>> > >>> > 1: ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = >>> > myBaseTy >>> > 2: makeLLDB(file.path(pkgPath, pkgName), compress = TRUE) >>> > 3: tools:::makeLazyLoadDB(dataEnv, dbbase, compress = compress) >>> > 4: lazyLoadDBinsertVariable(vars[i], from, datafile, ascii, compress, >>> > envhook) >>> > 5: function (e) >>> > 6: lazyLoadDBinsertValue(data, datafile, ascii, compress, envhook) >>> > >>> > Selection: 1 >>> > Browse[1]> annotation[1:2,] >>> > ENTREZID PROBE ACCNUM GO >>> > [1,] "100008565" "10766774" NA NA >>> > [2,] "100034253" "10937540" NA "GO:0005525 at IEA;GO:0005622 at IEA" >>> > PMID SYMBOL >>> > [1,] "16804107;17292978" "Slc39a4l" >>> > [2,] "8889548" "Gnl3l" >>> > GENENAME CHR >>> > [1,] "solute carrier family 39 (zinc transporter), member 4-like" NA >>> > [2,] "guanine nucleotide binding protein-like 3 (nucleolar)-like" "X" >>> > MAP REFSEQ UNIGENE CHRLOC PATH >>> > [1,] NA "NM_001101021;NP_001094491" "Rn.10120" "NA" NA >>> > [2,] "Xq14-q21" "NM_001081958;NP_001075427" "Rn.164274" "-40301218 at X" NA >>> > ENZYME PFAM PROSITE >>> > [1,] NA "NA at IPI00817057" "NA at IPI00817057" >>> > [2,] NA "PF01926 at IPI00362844" "NA at IPI00362844" >>> > ------------------------------------------------------------ >>> > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >>> > Indiana University School of Medicine >>> > >>> > 15032 Hunter Court, Westfield, IN 46074 >>> > >>> > (317) 490-5129 Work, & Mobile & VoiceMail >>> > (317) 399-1219 Home >>> > Skype: mkimpel >>> > >>> > "The real problem is not whether machines think but whether men do." -- B. >>> > F. Skinner >>> > ****************************************************************** >>> > >>> > [[alternative HTML version deleted]] >>> > >>> > _______________________________________________ >>> > Bioconductor mailing list >>> > Bioconductor at stat.math.ethz.ch >>> > https://stat.ethz.ch/mailman/listinfo/bioconductor >>> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> > >>> > >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >
ADD REPLYlink written 10.9 years ago by Mark W Kimpel830
Answer: newbie problems with AnnBuilder
0
gravatar for Sean Davis
10.9 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Tue, Oct 21, 2008 at 5:37 PM, Mark Kimpel <mwkimpel at="" gmail.com=""> wrote: > I'm having problems getting AnnBuilder to work with the Affy Rat Gene ST > array data supplied by Affy. Hi, Mark. This doesn't answer your question, but you might try using AnnotationDbi and, specifically, SQLForge, to create your annotation package. The packages built by AnnBuilder are deprecated and as of the new release, defunct. Sean
ADD COMMENTlink written 10.9 years ago by Sean Davis21k
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