problem with downloading dataset using GEOquery
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@kishor-tappita-2563
Last seen 10.3 years ago
Dear List, When I am trying to download a dataset from GEO. I get the below error at the end of my command session. > dataset2 <- getGEO("GSE12885") File stored at: C:\DOCUME~1\WELCOM~1\LOCALS~1\Temp\RtmpYy3CGa/GPL5082.soft Error in txt[i] <- readLines(con, 1) : replacement has length zero > sessionInfo() R version 2.9.2 (2009-08-24) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GEOquery_2.8.0 RCurl_0.98-1 bitops_1.0-4.1 Biobase_2.4.1 loaded via a namespace (and not attached): [1] AnnotationDbi_1.6.1 DBI_0.2-4 graph_1.22.2 [4] grid_2.9.2 lattice_0.17-25 RSQLite_0.7-2 [7] SparseM_0.80 tools_2.9.2 topGO_1.12.0 Thanks, Kishor
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@sean-davis-490
Last seen 4 months ago
United States
On Mon, Oct 5, 2009 at 9:03 AM, Kishor Tappita <kishor.tappita at="" gmail.com=""> wrote: > Dear List, > > When I am trying to download ?a dataset from GEO. I get the below > error at the end of my > command session. > >> dataset2 <- getGEO("GSE12885") > > > File stored at: C:\DOCUME~1\WELCOM~1\LOCALS~1\Temp\RtmpYy3CGa/GPL5082.soft > Error in txt[i] <- readLines(con, 1) : replacement has length zero Hi, Kishor. This is a problem with the GEO records for GPL5082. In particular, they are empty. I don't know if GEO meant for this to be so or not, but I was not aware that such empty records were acceptable in GEO. I'll follow up with the GEO staff to see what the deal is. Sean
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Dear Sean, Thank you so much for your reply and for letting me know the reason. I will eagerly wait for the GEO team to fix the problem. Thanks, Kishor On Mon, Oct 5, 2009 at 6:46 PM, Sean Davis <seandavi at="" gmail.com=""> wrote: > On Mon, Oct 5, 2009 at 9:03 AM, Kishor Tappita <kishor.tappita at="" gmail.com=""> wrote: >> Dear List, >> >> When I am trying to download ?a dataset from GEO. I get the below >> error at the end of my >> command session. >> >>> dataset2 <- getGEO("GSE12885") >> >> >> File stored at: C:\DOCUME~1\WELCOM~1\LOCALS~1\Temp\RtmpYy3CGa/GPL5082.soft >> Error in txt[i] <- readLines(con, 1) : replacement has length zero > > Hi, Kishor. ?This is a problem with the GEO records for GPL5082. ?In > particular, they are empty. ?I don't know if GEO meant for this to be > so or not, but I was not aware that such empty records were acceptable > in GEO. ?I'll follow up with the GEO staff to see what the deal is. > > Sean >
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On Mon, Oct 5, 2009 at 11:35 AM, Kishor Tappita <kishor.tappita@gmail.com> wrote: > Dear Sean, > > Thank you so much for your reply and for letting me know the reason. I > will eagerly wait > for the GEO team to fix the problem. Thanks for the patience, Kishor. Here is what the GEO team had to say: We do allow table-less Samples for tiling/promoter arrays. Some submitters do not generate normalized data for these types of Platforms. If processed data is available, we usually receive BED/BAR and TAS files which we link to the Sample record. In this particular case, the submitter supplied processed data on Series record GSE12864 (GSE12864 is part of superSeries GSE12885). So, I have made changes to GEOquery to deal with such GSEs, GPLs, and GSMs. These changes (version 2.9.6) will be available in the development branch in the next 1-2 days as the build system catches the changes. Sean > On Mon, Oct 5, 2009 at 6:46 PM, Sean Davis <seandavi@gmail.com> wrote: >> On Mon, Oct 5, 2009 at 9:03 AM, Kishor Tappita <kishor.tappita@gmail.com> wrote: >>> Dear List, >>> >>> When I am trying to download a dataset from GEO. I get the below >>> error at the end of my >>> command session. >>> >>>> dataset2 <- getGEO("GSE12885") >>> >>> >>> File stored at: C:\DOCUME~1\WELCOM~1\LOCALS~1\Temp\RtmpYy3CGa/GPL5082.soft >>> Error in txt[i] <- readLines(con, 1) : replacement has length zero >> >> Hi, Kishor. This is a problem with the GEO records for GPL5082. In >> particular, they are empty. I don't know if GEO meant for this to be >> so or not, but I was not aware that such empty records were acceptable >> in GEO. I'll follow up with the GEO staff to see what the deal is. >> >> Sean >> > [[alternative HTML version deleted]]
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Dear Sean, Sorry for the delayed response. I was on leave yesterday. Thank you so much for willing to make the change. Regards, Kishor On Tue, Oct 6, 2009 at 9:04 PM, Sean Davis <seandavi at="" gmail.com=""> wrote: > > > On Mon, Oct 5, 2009 at 11:35 AM, Kishor Tappita <kishor.tappita at="" gmail.com=""> > wrote: >> Dear Sean, >> >> Thank you so much for your reply and for letting me know the reason. I >> will eagerly wait >> for the GEO team to fix the problem. > > Thanks for the patience, Kishor. ?Here is what the GEO team had to say: > > We do allow table-less Samples for tiling/promoter arrays. Some submitters > do > not generate normalized data for these types of Platforms. If processed data > is available, we usually receive BED/BAR and TAS files which we link to the > Sample record. In this particular case, the submitter supplied processed > data > on Series record GSE12864 (GSE12864 is part of superSeries GSE12885). > > So, I have made changes to GEOquery to deal with such GSEs, GPLs, and GSMs. > These changes (version 2.9.6) will be available in the development branch in > the next 1-2 days as the build system catches the changes. > > Sean > >> On Mon, Oct 5, 2009 at 6:46 PM, Sean Davis <seandavi at="" gmail.com=""> wrote: >>> On Mon, Oct 5, 2009 at 9:03 AM, Kishor Tappita <kishor.tappita at="" gmail.com=""> >>> wrote: >>>> Dear List, >>>> >>>> When I am trying to download ?a dataset from GEO. I get the below >>>> error at the end of my >>>> command session. >>>> >>>>> dataset2 <- getGEO("GSE12885") >>>> >>>> >>>> File stored at: >>>> C:\DOCUME~1\WELCOM~1\LOCALS~1\Temp\RtmpYy3CGa/GPL5082.soft >>>> Error in txt[i] <- readLines(con, 1) : replacement has length zero >>> >>> Hi, Kishor. ?This is a problem with the GEO records for GPL5082. ?In >>> particular, they are empty. ?I don't know if GEO meant for this to be >>> so or not, but I was not aware that such empty records were acceptable >>> in GEO. ?I'll follow up with the GEO staff to see what the deal is. >>> >>> Sean >>> >> > >
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