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Question: troubles with GEOquery
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gravatar for Pascal Barbry
10.6 years ago by
Pascal Barbry10 wrote:
Hi all, I have troubles trying to download GSE files from GEO: library(GEOquery) GSE6281 <- getGEO("GSE6281", GSEMatrix = FALSE). Surprisingly, the example found in the help file is working nicely: gse <- getGEO("GSE462", GSEMatrix = FALSE) ?????!!!............. My troubles started after switching to the new version of Bioconductor. As I am using a Windows OS and that some of the getGEO options are not windows-proof, I was wondering if any others had experienced a similar situation? Any idea (outside swtching to Linux) would be appreciated. Thanks in advance, Pascal > sessionInfo() R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY= French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GEOquery_2.4.0 RCurl_0.9-2 Biobase_2.0.1
ADD COMMENTlink modified 10.6 years ago by Sean Davis21k • written 10.6 years ago by Pascal Barbry10
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gravatar for Sean Davis
10.6 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Fri, May 9, 2008 at 6:34 PM, Pascal Barbry <barbry at="" ipmc.cnrs.fr=""> wrote: > Hi all, > I have troubles trying to download GSE files from GEO: > library(GEOquery) > GSE6281 <- getGEO("GSE6281", GSEMatrix = FALSE). > > Surprisingly, the example found in the help file is working nicely: > gse <- getGEO("GSE462", GSEMatrix = FALSE) > > ?????!!!............. > > My troubles started after switching to the new version of Bioconductor. As I > am using a Windows OS and that some of the getGEO options are not > windows-proof, I was wondering if any others had experienced a similar > situation? Any idea (outside swtching to Linux) would be appreciated. Hi, Pascal. What problems are you having? You didn't give a report of the errors that you received. Sean >> sessionInfo() > R version 2.7.0 (2008-04-22) > i386-pc-mingw32 > > locale: > LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETAR Y=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] GEOquery_2.4.0 RCurl_0.9-2 Biobase_2.0.1 > > _______________________________________________ > 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 10.6 years ago by Sean Davis21k
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gravatar for Sean Davis
10.6 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
2008/5/10 Pascal Barbry <barbry at="" ipmc.cnrs.fr="">: > Hello Sean, > Sorry about that! The SOFT file seems correctly downloaded, then the > processor works full speed for hours (parsing the file???), and I am loosing > the access to the R console. I left once overnight and nothing better > happened. This is why I was unable to send error messages. I will re-run the > same command and I will forward them to you. Is there a reason to not use GSEMatrix=TRUE? That will be significantly faster. Over a wireless, it takes about 30 seconds. When parsing the entire SOFT file, it could take several hours. I noticed that there are supplementary .CEL files available, also. You could use getGEOSuppFiles() to download those and process them local using Bioconductor tools. Let me know if you have further questions. Sean > Sean Davis a ?crit : >> >> On Fri, May 9, 2008 at 6:34 PM, Pascal Barbry <barbry at="" ipmc.cnrs.fr=""> wrote: >>> >>> Hi all, >>> I have troubles trying to download GSE files from GEO: >>> library(GEOquery) >>> GSE6281 <- getGEO("GSE6281", GSEMatrix = FALSE). >>> >>> Surprisingly, the example found in the help file is working nicely: >>> gse <- getGEO("GSE462", GSEMatrix = FALSE) >>> >>> ?????!!!............. >>> >>> My troubles started after switching to the new version of Bioconductor. >>> As I >>> am using a Windows OS and that some of the getGEO options are not >>> windows-proof, I was wondering if any others had experienced a similar >>> situation? Any idea (outside swtching to Linux) would be appreciated. >> >> Hi, Pascal. What problems are you having? You didn't give a report >> of the errors that you received. >> >> Sean >> >> >>>> sessionInfo() >>> >>> R version 2.7.0 (2008-04-22) >>> i386-pc-mingw32 >>> >>> locale: >>> >>> LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONET ARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 >>> >>> attached base packages: >>> [1] tools stats graphics grDevices utils datasets methods >>> [8] base >>> >>> other attached packages: >>> [1] GEOquery_2.4.0 RCurl_0.9-2 Biobase_2.0.1 >>> >>> _______________________________________________ >>> 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 >>> >>> >>> ------------------------------------------------------------------ ------ >>> >>> >>> No virus found in this incoming message. >>> Checked by AVG. Version: 8.0.100 / Virus Database: 269.23.14/1425 - >>> Release Date: 09/05/2008 12:38 >
ADD COMMENTlink written 10.6 years ago by Sean Davis21k
0
gravatar for Sean Davis
10.6 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
2008/5/11 Pascal Barbry <barbry at="" ipmc.cnrs.fr="">: > Hello Sean, > I tried again after having clean a lot my disk, and reinstalling everything. > This time, it worked!... > I did not succeed with the GSEmatrix option turned to TRUE. So, if you don't mind, what do you mean by "did not succeed"? Did you receive an error? If so, what was it? It really helps me to know these things so that if there is a bug, I can fix it. > Here is the script and message from the console: > >>> Sys.time() >> >> [1] "2008-05-11 17:14:19 CEST" >>> >>> GSE7216 <- getGEO("GSE7216", GSEMatrix = FALSE) >> >> essai de l'URL >> 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/by_series/GSE7216/GSE7216 _family.soft.gz' >> ftp data connection made, file length 13316485 bytes >> URL ouverte >> downloaded 12.7 Mb >> >> File stored at: C:\DOCUME~1\Pascal\LOCALS~1\Temp\RtmpiH1ZtG/GSE7216.soft >> Parsing.... >> ^PLATFORM = GPL570 >> ^SAMPLE = GSM173533 >> ^SAMPLE = GSM173534 >> ^SAMPLE = GSM173535 >> ^SAMPLE = GSM173536 >> ^SAMPLE = GSM173537 >> ^SAMPLE = GSM173538 >> ^SAMPLE = GSM173539 >> ^SAMPLE = GSM173540 >> ^SAMPLE = GSM173541 >> ^SAMPLE = GSM173542 >> ^SAMPLE = GSM173543 >> ^SAMPLE = GSM173544 >> ^SAMPLE = GSM173545 >> ^SAMPLE = GSM173546 >> ^SAMPLE = GSM173547 >> ^SAMPLE = GSM173548 >> ^SAMPLE = GSM173549 >> ^SAMPLE = GSM173550 >> ^SAMPLE = GSM173551 >> ^SAMPLE = GSM173552 >> ^SAMPLE = GSM173553 >> ^SAMPLE = GSM173554 >> ^SAMPLE = GSM173555 >> ^SAMPLE = GSM173556 >>> >>> Sys.time() >> >> [1] "2008-05-11 17:49:20 CEST" >>> >>> > > As you can notice, it took about 35 minutes to download (around 5 minutes), > then parse the file (30 minutes). Yes, the files are large and the parsing is slow. Sean > Pascal > > > Sean Davis a ?crit : >> >> On Fri, May 9, 2008 at 6:34 PM, Pascal Barbry <barbry at="" ipmc.cnrs.fr=""> wrote: >>> >>> Hi all, >>> I have troubles trying to download GSE files from GEO: >>> library(GEOquery) >>> GSE6281 <- getGEO("GSE6281", GSEMatrix = FALSE). >>> >>> Surprisingly, the example found in the help file is working nicely: >>> gse <- getGEO("GSE462", GSEMatrix = FALSE) >>> >>> ?????!!!............. >>> >>> My troubles started after switching to the new version of Bioconductor. >>> As I >>> am using a Windows OS and that some of the getGEO options are not >>> windows-proof, I was wondering if any others had experienced a similar >>> situation? Any idea (outside swtching to Linux) would be appreciated. >> >> Hi, Pascal. What problems are you having? You didn't give a report >> of the errors that you received. >> >> Sean >> >> >>>> sessionInfo() >>> >>> R version 2.7.0 (2008-04-22) >>> i386-pc-mingw32 >>> >>> locale: >>> >>> LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONET ARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 >>> >>> attached base packages: >>> [1] tools stats graphics grDevices utils datasets methods >>> [8] base >>> >>> other attached packages: >>> [1] GEOquery_2.4.0 RCurl_0.9-2 Biobase_2.0.1 >>> >>> _______________________________________________ >>> 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 >>> >>> >>> ------------------------------------------------------------------ ------ >>> >>> >>> No virus found in this incoming message. >>> Checked by AVG. Version: 8.0.100 / Virus Database: 269.23.14/1425 - >>> Release Date: 09/05/2008 12:38 >
ADD COMMENTlink written 10.6 years ago by Sean Davis21k
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