GEOquery and GSE error
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Voke AO ▴ 760
@voke-ao-4830
Last seen 7.1 years ago
Hi all, I am unable to access a series file even though I get a message that it saved to a local directory, albeit with an error message and a number of warnings, after retrieval with GEOquery. Any ideas as to what I may be doing wrong? Thanks. Avoks > gse9006 = getGEO("GSE9006", GSEMatrix = TRUE) Found 2 file(s) GSE9006-GPL96_series_matrix.txt.gz trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE9006/G SE9006-GPL96_series_matrix.txt.gz' ftp data connection made, file length 5775933 bytes opened URL downloaded 5.5 Mb File stored at: C:\...\Temp\RtmpJM0ZOp/GPL96.soft Error in validObject(.Object) : invalid class "ExpressionSet" object: featureNames differ between assayData and featureData In addition: Warning messages: 1: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) : seek on a gzfile connection returned an internal error 2: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) : seek on a gzfile connection returned an internal error 3: In readLines(con, 1) : seek on a gzfile connection returned an internal error 4: In read.table(file = file, header = header, sep = sep, quote = quote, : seek on a gzfile connection returned an internal error 5: In read.table(file = file, header = header, sep = sep, quote = quote, : seek on a gzfile connection returned an internal error 6: In read.table(file = file, header = header, sep = sep, quote = quote, : seek on a gzfile connection returned an internal error 7: In read.table(file = file, header = header, sep = sep, quote = quote, : not all columns named in 'colClasses' exist > gse9006 Error: object 'gse9006' not found > show(gse9006) Error in show(gse9006) : error in evaluating the argument 'object' in selecting a method for function 'show': Error: object 'gse9006' not found
GEOquery GEOquery • 1.4k views
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@sean-davis-490
Last seen 24 days ago
United States
Hi, Avoks. Without sessionInfo(), it is not possible to be sure what version of GEOquery you are running, but I would suggest you upgrade to the newest version of GEOquery. I think that will fix the issue. Sorry for the inconvenience. Sean On Tue, Sep 20, 2011 at 9:24 AM, Ovokeraye Achinike-Oduaran <ovokeraye at="" gmail.com=""> wrote: > Hi all, > > I am unable to access a series file even though I get a message that > it saved to a local directory, albeit with an error message and a > number of warnings, after retrieval with GEOquery. Any ideas as to > what I may be doing wrong? > > Thanks. > > Avoks > >> gse9006 = getGEO("GSE9006", GSEMatrix = TRUE) > Found 2 file(s) > GSE9006-GPL96_series_matrix.txt.gz > trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE9006 /GSE9006-GPL96_series_matrix.txt.gz' > ftp data connection made, file length 5775933 bytes > opened URL > downloaded 5.5 Mb > > File stored at: > C:\...\Temp\RtmpJM0ZOp/GPL96.soft > Error in validObject(.Object) : > ?invalid class "ExpressionSet" object: featureNames differ between > assayData and featureData > In addition: Warning messages: > 1: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) : > ?seek on a gzfile connection returned an internal error > 2: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) : > ?seek on a gzfile connection returned an internal error > 3: In readLines(con, 1) : > ?seek on a gzfile connection returned an internal error > 4: In read.table(file = file, header = header, sep = sep, quote = quote, ?: > ?seek on a gzfile connection returned an internal error > 5: In read.table(file = file, header = header, sep = sep, quote = quote, ?: > ?seek on a gzfile connection returned an internal error > 6: In read.table(file = file, header = header, sep = sep, quote = quote, ?: > ?seek on a gzfile connection returned an internal error > 7: In read.table(file = file, header = header, sep = sep, quote = quote, ?: > ?not all columns named in 'colClasses' exist > >> gse9006 > Error: object 'gse9006' not found > >> show(gse9006) > Error in show(gse9006) : > ?error in evaluating the argument 'object' in selecting a method for > function 'show': Error: object 'gse9006' not found > > _______________________________________________ > 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 Sean, Thanks. I'm thinking I have the latest version because I only very recently installed the package. [1] GEOquery_2.19.3 Biobase_2.12.2 . Is there a more recent one? Thanks. Avoks On Tue, Sep 20, 2011 at 3:37 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > Hi, Avoks. > > Without sessionInfo(), it is not possible to be sure what version of > GEOquery you are running, but I would suggest you upgrade to the > newest version of GEOquery. ?I think that will fix the issue. > > Sorry for the inconvenience. > > Sean > > > On Tue, Sep 20, 2011 at 9:24 AM, Ovokeraye Achinike-Oduaran > <ovokeraye at="" gmail.com=""> wrote: >> Hi all, >> >> I am unable to access a series file even though I get a message that >> it saved to a local directory, albeit with an error message and a >> number of warnings, after retrieval with GEOquery. Any ideas as to >> what I may be doing wrong? >> >> Thanks. >> >> Avoks >> >>> gse9006 = getGEO("GSE9006", GSEMatrix = TRUE) >> Found 2 file(s) >> GSE9006-GPL96_series_matrix.txt.gz >> trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE900 6/GSE9006-GPL96_series_matrix.txt.gz' >> ftp data connection made, file length 5775933 bytes >> opened URL >> downloaded 5.5 Mb >> >> File stored at: >> C:\...\Temp\RtmpJM0ZOp/GPL96.soft >> Error in validObject(.Object) : >> ?invalid class "ExpressionSet" object: featureNames differ between >> assayData and featureData >> In addition: Warning messages: >> 1: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) : >> ?seek on a gzfile connection returned an internal error >> 2: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) : >> ?seek on a gzfile connection returned an internal error >> 3: In readLines(con, 1) : >> ?seek on a gzfile connection returned an internal error >> 4: In read.table(file = file, header = header, sep = sep, quote = quote, ?: >> ?seek on a gzfile connection returned an internal error >> 5: In read.table(file = file, header = header, sep = sep, quote = quote, ?: >> ?seek on a gzfile connection returned an internal error >> 6: In read.table(file = file, header = header, sep = sep, quote = quote, ?: >> ?seek on a gzfile connection returned an internal error >> 7: In read.table(file = file, header = header, sep = sep, quote = quote, ?: >> ?not all columns named in 'colClasses' exist >> >>> gse9006 >> Error: object 'gse9006' not found >> >>> show(gse9006) >> Error in show(gse9006) : >> ?error in evaluating the argument 'object' in selecting a method for >> function 'show': Error: object 'gse9006' not found >> >> _______________________________________________ >> 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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On Tue, Sep 20, 2011 at 9:44 AM, Ovokeraye Achinike-Oduaran <ovokeraye at="" gmail.com=""> wrote: > Hi Sean, > > Thanks. I'm thinking I have the latest version because I only very > recently installed the package. > > [1] GEOquery_2.19.3 Biobase_2.12.2 . > > Is there a more recent one? Yes. 2.19.4 is the most recent version. Sean > On Tue, Sep 20, 2011 at 3:37 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >> Hi, Avoks. >> >> Without sessionInfo(), it is not possible to be sure what version of >> GEOquery you are running, but I would suggest you upgrade to the >> newest version of GEOquery. ?I think that will fix the issue. >> >> Sorry for the inconvenience. >> >> Sean >> >> >> On Tue, Sep 20, 2011 at 9:24 AM, Ovokeraye Achinike-Oduaran >> <ovokeraye at="" gmail.com=""> wrote: >>> Hi all, >>> >>> I am unable to access a series file even though I get a message that >>> it saved to a local directory, albeit with an error message and a >>> number of warnings, after retrieval with GEOquery. Any ideas as to >>> what I may be doing wrong? >>> >>> Thanks. >>> >>> Avoks >>> >>>> gse9006 = getGEO("GSE9006", GSEMatrix = TRUE) >>> Found 2 file(s) >>> GSE9006-GPL96_series_matrix.txt.gz >>> trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE90 06/GSE9006-GPL96_series_matrix.txt.gz' >>> ftp data connection made, file length 5775933 bytes >>> opened URL >>> downloaded 5.5 Mb >>> >>> File stored at: >>> C:\...\Temp\RtmpJM0ZOp/GPL96.soft >>> Error in validObject(.Object) : >>> ?invalid class "ExpressionSet" object: featureNames differ between >>> assayData and featureData >>> In addition: Warning messages: >>> 1: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) : >>> ?seek on a gzfile connection returned an internal error >>> 2: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) : >>> ?seek on a gzfile connection returned an internal error >>> 3: In readLines(con, 1) : >>> ?seek on a gzfile connection returned an internal error >>> 4: In read.table(file = file, header = header, sep = sep, quote = quote, ?: >>> ?seek on a gzfile connection returned an internal error >>> 5: In read.table(file = file, header = header, sep = sep, quote = quote, ?: >>> ?seek on a gzfile connection returned an internal error >>> 6: In read.table(file = file, header = header, sep = sep, quote = quote, ?: >>> ?seek on a gzfile connection returned an internal error >>> 7: In read.table(file = file, header = header, sep = sep, quote = quote, ?: >>> ?not all columns named in 'colClasses' exist >>> >>>> gse9006 >>> Error: object 'gse9006' not found >>> >>>> show(gse9006) >>> Error in show(gse9006) : >>> ?error in evaluating the argument 'object' in selecting a method for >>> function 'show': Error: object 'gse9006' not found >>> >>> _______________________________________________ >>> 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 >>> >> > > _______________________________________________ > 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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@sean-davis-490
Last seen 24 days ago
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On Tue, Sep 20, 2011 at 10:19 AM, Ovokeraye Achinike-Oduaran <ovokeraye at="" gmail.com=""> wrote: > Okay, thanks Sean. I used the update.packages() in the R window, and > when I restarted R and tried loading the GEOquery library, this is > what I got. > >> library(GEOquery) > Loading required package: Biobase > > Welcome to Bioconductor > > ?Vignettes contain introductory material. To view, type > ?'browseVignettes()'. To cite Bioconductor, see > ?'citation("Biobase")' and for packages 'citation("pkgname")'. > > Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) : > ?there is no package called 'RCurl' Looks like you will need to install RCurl. Sean > In addition: Warning message: > '.readRDS' is deprecated. > Use 'readRDS' instead. > See help("Deprecated") > Error: package/namespace load failed for 'GEOquery' > > Is it something I'm doing wrong at my end? > > Thanks again. > > > > On Tue, Sep 20, 2011 at 3:50 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >> On Tue, Sep 20, 2011 at 9:44 AM, Ovokeraye Achinike-Oduaran >> <ovokeraye at="" gmail.com=""> wrote: >>> Hi Sean, >>> >>> Thanks. I'm thinking I have the latest version because I only very >>> recently installed the package. >>> >>> [1] GEOquery_2.19.3 Biobase_2.12.2 . >>> >>> Is there a more recent one? >> >> Yes. ?2.19.4 is the most recent version. >> >> Sean >> >> >>> On Tue, Sep 20, 2011 at 3:37 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >>>> Hi, Avoks. >>>> >>>> Without sessionInfo(), it is not possible to be sure what version of >>>> GEOquery you are running, but I would suggest you upgrade to the >>>> newest version of GEOquery. ?I think that will fix the issue. >>>> >>>> Sorry for the inconvenience. >>>> >>>> Sean >>>> >>>> >>>> On Tue, Sep 20, 2011 at 9:24 AM, Ovokeraye Achinike-Oduaran >>>> <ovokeraye at="" gmail.com=""> wrote: >>>>> Hi all, >>>>> >>>>> I am unable to access a series file even though I get a message that >>>>> it saved to a local directory, albeit with an error message and a >>>>> number of warnings, after retrieval with GEOquery. Any ideas as to >>>>> what I may be doing wrong? >>>>> >>>>> Thanks. >>>>> >>>>> Avoks >>>>> >>>>>> gse9006 = getGEO("GSE9006", GSEMatrix = TRUE) >>>>> Found 2 file(s) >>>>> GSE9006-GPL96_series_matrix.txt.gz >>>>> trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE 9006/GSE9006-GPL96_series_matrix.txt.gz' >>>>> ftp data connection made, file length 5775933 bytes >>>>> opened URL >>>>> downloaded 5.5 Mb >>>>> >>>>> File stored at: >>>>> C:\...\Temp\RtmpJM0ZOp/GPL96.soft >>>>> Error in validObject(.Object) : >>>>> ?invalid class "ExpressionSet" object: featureNames differ between >>>>> assayData and featureData >>>>> In addition: Warning messages: >>>>> 1: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) : >>>>> ?seek on a gzfile connection returned an internal error >>>>> 2: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) : >>>>> ?seek on a gzfile connection returned an internal error >>>>> 3: In readLines(con, 1) : >>>>> ?seek on a gzfile connection returned an internal error >>>>> 4: In read.table(file = file, header = header, sep = sep, quote = quote, ?: >>>>> ?seek on a gzfile connection returned an internal error >>>>> 5: In read.table(file = file, header = header, sep = sep, quote = quote, ?: >>>>> ?seek on a gzfile connection returned an internal error >>>>> 6: In read.table(file = file, header = header, sep = sep, quote = quote, ?: >>>>> ?seek on a gzfile connection returned an internal error >>>>> 7: In read.table(file = file, header = header, sep = sep, quote = quote, ?: >>>>> ?not all columns named in 'colClasses' exist >>>>> >>>>>> gse9006 >>>>> Error: object 'gse9006' not found >>>>> >>>>>> show(gse9006) >>>>> Error in show(gse9006) : >>>>> ?error in evaluating the argument 'object' in selecting a method for >>>>> function 'show': Error: object 'gse9006' not found >>>>> >>>>> _______________________________________________ >>>>> 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 >>>>> >>>> >>> >>> _______________________________________________ >>> 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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Thanks Sean.I got RCurl installed but GEOquery doesn't update with the update.packages() or the specific update.packages("GEOquery") options. So, I'm still having the same challenge. -Avoks On Tue, Sep 20, 2011 at 4:22 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Tue, Sep 20, 2011 at 10:19 AM, Ovokeraye Achinike-Oduaran > <ovokeraye at="" gmail.com=""> wrote: >> Okay, thanks Sean. I used the update.packages() in the R window, and >> when I restarted R and tried loading the GEOquery library, this is >> what I got. >> >>> library(GEOquery) >> Loading required package: Biobase >> >> Welcome to Bioconductor >> >> ?Vignettes contain introductory material. To view, type >> ?'browseVignettes()'. To cite Bioconductor, see >> ?'citation("Biobase")' and for packages 'citation("pkgname")'. >> >> Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) : >> ?there is no package called 'RCurl' > > Looks like you will need to install RCurl. > > Sean > > >> In addition: Warning message: >> '.readRDS' is deprecated. >> Use 'readRDS' instead. >> See help("Deprecated") >> Error: package/namespace load failed for 'GEOquery' >> >> Is it something I'm doing wrong at my end? >> >> Thanks again. >> >> >> >> On Tue, Sep 20, 2011 at 3:50 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >>> On Tue, Sep 20, 2011 at 9:44 AM, Ovokeraye Achinike-Oduaran >>> <ovokeraye at="" gmail.com=""> wrote: >>>> Hi Sean, >>>> >>>> Thanks. I'm thinking I have the latest version because I only very >>>> recently installed the package. >>>> >>>> [1] GEOquery_2.19.3 Biobase_2.12.2 . >>>> >>>> Is there a more recent one? >>> >>> Yes. ?2.19.4 is the most recent version. >>> >>> Sean >>> >>> >>>> On Tue, Sep 20, 2011 at 3:37 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >>>>> Hi, Avoks. >>>>> >>>>> Without sessionInfo(), it is not possible to be sure what version of >>>>> GEOquery you are running, but I would suggest you upgrade to the >>>>> newest version of GEOquery. ?I think that will fix the issue. >>>>> >>>>> Sorry for the inconvenience. >>>>> >>>>> Sean >>>>> >>>>> >>>>> On Tue, Sep 20, 2011 at 9:24 AM, Ovokeraye Achinike-Oduaran >>>>> <ovokeraye at="" gmail.com=""> wrote: >>>>>> Hi all, >>>>>> >>>>>> I am unable to access a series file even though I get a message that >>>>>> it saved to a local directory, albeit with an error message and a >>>>>> number of warnings, after retrieval with GEOquery. Any ideas as to >>>>>> what I may be doing wrong? >>>>>> >>>>>> Thanks. >>>>>> >>>>>> Avoks >>>>>> >>>>>>> gse9006 = getGEO("GSE9006", GSEMatrix = TRUE) >>>>>> Found 2 file(s) >>>>>> GSE9006-GPL96_series_matrix.txt.gz >>>>>> trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GS E9006/GSE9006-GPL96_series_matrix.txt.gz' >>>>>> ftp data connection made, file length 5775933 bytes >>>>>> opened URL >>>>>> downloaded 5.5 Mb >>>>>> >>>>>> File stored at: >>>>>> C:\...\Temp\RtmpJM0ZOp/GPL96.soft >>>>>> Error in validObject(.Object) : >>>>>> ?invalid class "ExpressionSet" object: featureNames differ between >>>>>> assayData and featureData >>>>>> In addition: Warning messages: >>>>>> 1: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) : >>>>>> ?seek on a gzfile connection returned an internal error >>>>>> 2: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) : >>>>>> ?seek on a gzfile connection returned an internal error >>>>>> 3: In readLines(con, 1) : >>>>>> ?seek on a gzfile connection returned an internal error >>>>>> 4: In read.table(file = file, header = header, sep = sep, quote = quote, ?: >>>>>> ?seek on a gzfile connection returned an internal error >>>>>> 5: In read.table(file = file, header = header, sep = sep, quote = quote, ?: >>>>>> ?seek on a gzfile connection returned an internal error >>>>>> 6: In read.table(file = file, header = header, sep = sep, quote = quote, ?: >>>>>> ?seek on a gzfile connection returned an internal error >>>>>> 7: In read.table(file = file, header = header, sep = sep, quote = quote, ?: >>>>>> ?not all columns named in 'colClasses' exist >>>>>> >>>>>>> gse9006 >>>>>> Error: object 'gse9006' not found >>>>>> >>>>>>> show(gse9006) >>>>>> Error in show(gse9006) : >>>>>> ?error in evaluating the argument 'object' in selecting a method for >>>>>> function 'show': Error: object 'gse9006' not found >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>>> >>>>> >>>> >>>> _______________________________________________ >>>> 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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On Wed, Sep 21, 2011 at 3:13 AM, Ovokeraye Achinike-Oduaran <ovokeraye at="" gmail.com=""> wrote: > Thanks Sean.I got RCurl installed but GEOquery doesn't update with the > update.packages() or the specific update.packages("GEOquery") options. This should get the job done. source('http://bioconductor.org/biocLite.R') biocLite('GEOquery') Sean > So, I'm still having the same challenge. > > -Avoks > > On Tue, Sep 20, 2011 at 4:22 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >> On Tue, Sep 20, 2011 at 10:19 AM, Ovokeraye Achinike-Oduaran >> <ovokeraye at="" gmail.com=""> wrote: >>> Okay, thanks Sean. I used the update.packages() in the R window, and >>> when I restarted R and tried loading the GEOquery library, this is >>> what I got. >>> >>>> library(GEOquery) >>> Loading required package: Biobase >>> >>> Welcome to Bioconductor >>> >>> ?Vignettes contain introductory material. To view, type >>> ?'browseVignettes()'. To cite Bioconductor, see >>> ?'citation("Biobase")' and for packages 'citation("pkgname")'. >>> >>> Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) : >>> ?there is no package called 'RCurl' >> >> Looks like you will need to install RCurl. >> >> Sean >> >> >>> In addition: Warning message: >>> '.readRDS' is deprecated. >>> Use 'readRDS' instead. >>> See help("Deprecated") >>> Error: package/namespace load failed for 'GEOquery' >>> >>> Is it something I'm doing wrong at my end? >>> >>> Thanks again. >>> >>> >>> >>> On Tue, Sep 20, 2011 at 3:50 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >>>> On Tue, Sep 20, 2011 at 9:44 AM, Ovokeraye Achinike-Oduaran >>>> <ovokeraye at="" gmail.com=""> wrote: >>>>> Hi Sean, >>>>> >>>>> Thanks. I'm thinking I have the latest version because I only very >>>>> recently installed the package. >>>>> >>>>> [1] GEOquery_2.19.3 Biobase_2.12.2 . >>>>> >>>>> Is there a more recent one? >>>> >>>> Yes. ?2.19.4 is the most recent version. >>>> >>>> Sean >>>> >>>> >>>>> On Tue, Sep 20, 2011 at 3:37 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >>>>>> Hi, Avoks. >>>>>> >>>>>> Without sessionInfo(), it is not possible to be sure what version of >>>>>> GEOquery you are running, but I would suggest you upgrade to the >>>>>> newest version of GEOquery. ?I think that will fix the issue. >>>>>> >>>>>> Sorry for the inconvenience. >>>>>> >>>>>> Sean >>>>>> >>>>>> >>>>>> On Tue, Sep 20, 2011 at 9:24 AM, Ovokeraye Achinike-Oduaran >>>>>> <ovokeraye at="" gmail.com=""> wrote: >>>>>>> Hi all, >>>>>>> >>>>>>> I am unable to access a series file even though I get a message that >>>>>>> it saved to a local directory, albeit with an error message and a >>>>>>> number of warnings, after retrieval with GEOquery. Any ideas as to >>>>>>> what I may be doing wrong? >>>>>>> >>>>>>> Thanks. >>>>>>> >>>>>>> Avoks >>>>>>> >>>>>>>> gse9006 = getGEO("GSE9006", GSEMatrix = TRUE) >>>>>>> Found 2 file(s) >>>>>>> GSE9006-GPL96_series_matrix.txt.gz >>>>>>> trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/G SE9006/GSE9006-GPL96_series_matrix.txt.gz' >>>>>>> ftp data connection made, file length 5775933 bytes >>>>>>> opened URL >>>>>>> downloaded 5.5 Mb >>>>>>> >>>>>>> File stored at: >>>>>>> C:\...\Temp\RtmpJM0ZOp/GPL96.soft >>>>>>> Error in validObject(.Object) : >>>>>>> ?invalid class "ExpressionSet" object: featureNames differ between >>>>>>> assayData and featureData >>>>>>> In addition: Warning messages: >>>>>>> 1: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) : >>>>>>> ?seek on a gzfile connection returned an internal error >>>>>>> 2: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) : >>>>>>> ?seek on a gzfile connection returned an internal error >>>>>>> 3: In readLines(con, 1) : >>>>>>> ?seek on a gzfile connection returned an internal error >>>>>>> 4: In read.table(file = file, header = header, sep = sep, quote = quote, ?: >>>>>>> ?seek on a gzfile connection returned an internal error >>>>>>> 5: In read.table(file = file, header = header, sep = sep, quote = quote, ?: >>>>>>> ?seek on a gzfile connection returned an internal error >>>>>>> 6: In read.table(file = file, header = header, sep = sep, quote = quote, ?: >>>>>>> ?seek on a gzfile connection returned an internal error >>>>>>> 7: In read.table(file = file, header = header, sep = sep, quote = quote, ?: >>>>>>> ?not all columns named in 'colClasses' exist >>>>>>> >>>>>>>> gse9006 >>>>>>> Error: object 'gse9006' not found >>>>>>> >>>>>>>> show(gse9006) >>>>>>> Error in show(gse9006) : >>>>>>> ?error in evaluating the argument 'object' in selecting a method for >>>>>>> function 'show': Error: object 'gse9006' not found >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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 >>>>>>> >>>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>>> >>>> >>> >> > > _______________________________________________ > 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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