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Question: GEOquery and GSE error
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gravatar for Voke AO
6.9 years ago by
Voke AO760
Voke AO760 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/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
ADD COMMENTlink modified 6.9 years ago by Sean Davis21k • written 6.9 years ago by Voke AO760
0
gravatar for Sean Davis
6.9 years ago by
Sean Davis21k
United States
Sean Davis21k 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/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 >
ADD COMMENTlink written 6.9 years ago by Sean Davis21k
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 >> >
ADD REPLYlink written 6.9 years ago by Voke AO760
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 >
ADD REPLYlink written 6.9 years ago by Sean Davis21k
0
gravatar for Sean Davis
6.9 years ago by
Sean Davis21k
United States
Sean Davis21k 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/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 >>> >> >
ADD COMMENTlink written 6.9 years ago by Sean Davis21k
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 >>>> >>> >> >
ADD REPLYlink written 6.9 years ago by Voke AO760
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 >
ADD REPLYlink written 6.9 years ago by Sean Davis21k
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