GEOquery not parsing GSE expression sets
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@lucas-santana-dos-santos-5873
Last seen 9.6 years ago
All, I have been trying to use the function getGEO, part of GEOquery package to retrieve GSE objects. However, I am getting the following error message: data/GEO> gse2553 <- getGEO('GSE2553',GSEMatrix=TRUE) Found 1 file(s) GSE2553_series_matrix.txt.gz Using locally cached version: /var/folders/z4/hzbhqd1j3gzc4mqhq29fqb24 0000gr/T//Rtmpb3s3hN/GSE2553_series_matrix.txt.gz Error in `row.names<-.data.frame`(`*tmp*`, value = value) : invalid 'row.names' length I get the same error no matter which GEO GSE id I use. It seems to be a parsing error, when creating a data frame This was suppose to work, as this code snippet is from the "Using the GEOquery package" PDF (page 13: http://www.bioconductor.org/packages/2 .11/bioc/vignettes/GEOquery/inst/doc/GEOquery.pdf). Any thoughts about what id the cause of error or how to fix it? Thank you very much, Lucas [[alternative HTML version deleted]]
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@sean-davis-490
Last seen 3 months ago
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On Thu, Apr 4, 2013 at 11:51 AM, Lucas Santana dos Santos <santanasantosl at="" me.com=""> wrote: > All, > > I have been trying to use the function getGEO, part of GEOquery package to retrieve GSE objects. > However, I am getting the following error message: > > data/GEO> gse2553 <- getGEO('GSE2553',GSEMatrix=TRUE) > Found 1 file(s) > GSE2553_series_matrix.txt.gz > Using locally cached version: /var/folders/z4/hzbhqd1j3gzc4mqhq29fqb 240000gr/T//Rtmpb3s3hN/GSE2553_series_matrix.txt.gz > Error in `row.names<-.data.frame`(`*tmp*`, value = value) : > invalid 'row.names' length > > I get the same error no matter which GEO GSE id I use. It seems to be a parsing error, when creating a data frame > This was suppose to work, as this code snippet is from the "Using the GEOquery package" PDF (page 13: http://www.bioconductor.org/packag es/2.11/bioc/vignettes/GEOquery/inst/doc/GEOquery.pdf). > > Any thoughts about what id the cause of error or how to fix it? Hi, Lucas. Could you send the output of sessionInfo()? Also, could you try this in a new R session? It appears that GEOquery is picking up a cached version of the series matrix file that might be corrupted. Sean > > Thank you very much, > > > Lucas > [[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 Sean, Here is my session info: R version 2.14.0 (2011-10-31) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.2.1 GEOquery_2.21.9 Biobase_2.14.0 mvbutils_2.5.101 loaded via a namespace (and not attached): [1] RCurl_1.91-1 XML_3.9-4 Thanks, Lucas On Apr 4, 2013, at 12:00 PM, Sean Davis wrote: > On Thu, Apr 4, 2013 at 11:51 AM, Lucas Santana dos Santos > <santanasantosl at="" me.com=""> wrote: >> All, >> >> I have been trying to use the function getGEO, part of GEOquery package to retrieve GSE objects. >> However, I am getting the following error message: >> >> data/GEO> gse2553 <- getGEO('GSE2553',GSEMatrix=TRUE) >> Found 1 file(s) >> GSE2553_series_matrix.txt.gz >> Using locally cached version: /var/folders/z4/hzbhqd1j3gzc4mqhq29fq b240000gr/T//Rtmpb3s3hN/GSE2553_series_matrix.txt.gz >> Error in `row.names<-.data.frame`(`*tmp*`, value = value) : >> invalid 'row.names' length >> >> I get the same error no matter which GEO GSE id I use. It seems to be a parsing error, when creating a data frame >> This was suppose to work, as this code snippet is from the "Using the GEOquery package" PDF (page 13: http://www.bioconductor.org/packag es/2.11/bioc/vignettes/GEOquery/inst/doc/GEOquery.pdf). >> >> Any thoughts about what id the cause of error or how to fix it? > > Hi, Lucas. > > Could you send the output of sessionInfo()? Also, could you try this > in a new R session? It appears that GEOquery is picking up a cached > version of the series matrix file that might be corrupted. > > Sean > >> >> Thank you very much, >> >> >> Lucas >> [[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 Sean, I think I might know the source of error. GEOquery works fine before I load the 'mvbutils' package. Once I load it I starting getting the error... Thanks, Lucas On Apr 4, 2013, at 12:00 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Thu, Apr 4, 2013 at 11:51 AM, Lucas Santana dos Santos > <santanasantosl at="" me.com=""> wrote: >> All, >> >> I have been trying to use the function getGEO, part of GEOquery package to retrieve GSE objects. >> However, I am getting the following error message: >> >> data/GEO> gse2553 <- getGEO('GSE2553',GSEMatrix=TRUE) >> Found 1 file(s) >> GSE2553_series_matrix.txt.gz >> Using locally cached version: /var/folders/z4/hzbhqd1j3gzc4mqhq29fq b240000gr/T//Rtmpb3s3hN/GSE2553_series_matrix.txt.gz >> Error in `row.names<-.data.frame`(`*tmp*`, value = value) : >> invalid 'row.names' length >> >> I get the same error no matter which GEO GSE id I use. It seems to be a parsing error, when creating a data frame >> This was suppose to work, as this code snippet is from the "Using the GEOquery package" PDF (page 13: http://www.bioconductor.org/packag es/2.11/bioc/vignettes/GEOquery/inst/doc/GEOquery.pdf). >> >> Any thoughts about what id the cause of error or how to fix it? > > Hi, Lucas. > > Could you send the output of sessionInfo()? Also, could you try this > in a new R session? It appears that GEOquery is picking up a cached > version of the series matrix file that might be corrupted. > > Sean > >> >> Thank you very much, >> >> >> Lucas >> [[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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On Thu, Apr 4, 2013 at 12:09 PM, Lucas Santana dos Santos <santanasantosl at="" me.com=""> wrote: > Hi Sean, > > I think I might know the source of error. GEOquery works fine before I load the 'mvbutils' package. > Once I load it I starting getting the error... I'll look into it. Thanks for the hint. Sean > Thanks, > > Lucas > > On Apr 4, 2013, at 12:00 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > >> On Thu, Apr 4, 2013 at 11:51 AM, Lucas Santana dos Santos >> <santanasantosl at="" me.com=""> wrote: >>> All, >>> >>> I have been trying to use the function getGEO, part of GEOquery package to retrieve GSE objects. >>> However, I am getting the following error message: >>> >>> data/GEO> gse2553 <- getGEO('GSE2553',GSEMatrix=TRUE) >>> Found 1 file(s) >>> GSE2553_series_matrix.txt.gz >>> Using locally cached version: /var/folders/z4/hzbhqd1j3gzc4mqhq29f qb240000gr/T//Rtmpb3s3hN/GSE2553_series_matrix.txt.gz >>> Error in `row.names<-.data.frame`(`*tmp*`, value = value) : >>> invalid 'row.names' length >>> >>> I get the same error no matter which GEO GSE id I use. It seems to be a parsing error, when creating a data frame >>> This was suppose to work, as this code snippet is from the "Using the GEOquery package" PDF (page 13: http://www.bioconductor.org/packag es/2.11/bioc/vignettes/GEOquery/inst/doc/GEOquery.pdf). >>> >>> Any thoughts about what id the cause of error or how to fix it? >> >> Hi, Lucas. >> >> Could you send the output of sessionInfo()? Also, could you try this >> in a new R session? It appears that GEOquery is picking up a cached >> version of the series matrix file that might be corrupted. >> >> Sean >> >>> >>> Thank you very much, >>> >>> >>> Lucas >>> [[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 > > _______________________________________________ > 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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