Error with GEOquery
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Sharon Anbu ▴ 480
@sharon-anbu-1524
Last seen 7.0 years ago
Hi Sean, I am trying to use GEOquery to download GSE data files from GEO. When I tried, I am getting the following error: gse <- getGEO("GSE2718") trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/data/geo/by_series/GSE2718/ GSE2718_family.soft.gz' ftp data connection made, file length 23892634 bytes opened URL downloaded 23332Kb File stored at: C:\DOCUME~1\Anbarasu\LOCALS~1\Temp\Rtmp8707/GSE2718.soft.gz Parsing.... ^PLATFORM = GPL2000 ^SAMPLE = GSM49820 ^SAMPLE = GSM65592 Error in regexpr(pattern, text, extended, fixed, useBytes) : invalid argument my sessionInfo: R version 2.2.0, 2005-10-06, i386-pc-mingw32 attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" "base" other attached packages: GEOquery "1.5.6" Is it due to my R 2.2.0? I am using GEOquery on Windows XP with 1GB RAM. And, another related question is: How can I use *getGEO() * with the already downloaded GSE2718.soft.gz file (to avoid subsequent downlaoding). Thanks in advance. Regards, Sharon
GEOquery GEOquery • 812 views
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@sean-davis-490
Last seen 16 days ago
United States
Hi, Sharon. It turns out that you found a bug in the way that GEO was preparing their GSE files. GSE2718 is fixed now and you should be able to use GEOquery again. If others see the same error, GEO passed along that the other GSE files should be fixed within a few days. As for using an already-downloaded file, see the "filename" argument in the getGEO() help. This will allow you to specify a filename of a previously downloaded file. Sean On 4/11/06 4:54 AM, "Sharon" <sharonanandhi at="" gmail.com=""> wrote: > Hi Sean, I am trying to use GEOquery to download GSE data files from GEO. > When I tried, I am getting the following error: gse <- > getGEO("GSE2718") trying URL > 'ftp://ftp.ncbi.nih.gov/pub/geo/data/geo/by_series/GSE2718/GSE2718_f amily.soft > .gz' ftp data connection made, file length 23892634 bytes opened > URL downloaded 23332Kb File stored > at: C:\DOCUME~1\Anbarasu\LOCALS~1\Temp\Rtmp8707/GSE2718.soft.gz Parsing.... ^P > LATFORM = GPL2000 ^SAMPLE = GSM49820 ^SAMPLE = GSM65592 Error in > regexpr(pattern, text, extended, fixed, useBytes) : invalid > argument my sessionInfo: R version 2.2.0, 2005-10-06, > i386-pc-mingw32 attached base packages: [1] "methods" "stats" > "graphics" "grDevices" "utils" "datasets" "base" other attached > packages: GEOquery "1.5.6" Is it due to my R 2.2.0? I am using GEOquery on > Windows XP with 1GB RAM. And, another related question is: How can I use > *getGEO() * with the already downloaded GSE2718.soft.gz file (to avoid > subsequent downlaoding). Thanks in advance. Regards, Sharon
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On 4/19/06 6:28 AM, "Sharon" <sharonanandhi at="" gmail.com=""> wrote: > Hi Sean, Thanks for your help and for your effort in developing this useful > tool. I have tried now and it works fine. I was able to create the exprSet > object (followed vignette) from GSE. There are few things that I didn't > understand. I would appreciate your help in this. 1. When I looked at VALUE, > it is mentioned that 'Log Ratio (not used)'. What does this mean? BTW, this 2 > color cDNA data set. All the information is supplied by the submitter (who in your case looks to be Rishi Khan). You will have to contact him/her about what information was used/not used in their analysis. The VALUE column typically represents log-transformed, normalized values, but GEO doesn't enforce that in any strict way. Your best bet is to contact the original submitter to clarify what data is meant to be useful. > 2. Since, all the samples of from GPL2000, I tried to > use getGEO("GPL2000") to access gene information for this chip. But i don't > know how to extract this info from GPL. Could you please provide some info on > this issue. Again, the platform information is supplied by the submitter. Looking at this GPL, it looks like the original submitter included only the "clone ID". You will probably need to take these clone IDs and pass them through something like: http://source.stanford.edu Just write out the clone id column from the GPL20000 by doing something like: gpl2000 <- GPLList(gse)[[1]] # the GPL information comes with the GSE --no need to download again write.table(Table(gpl2000)$CLONE_ID,file='rat.clone.id.txt',sep="\t",c ol.nam es=FALSE,row.names=FALSE,quote=FALSE) Then use the batch submission on source.stanford.edu to get the information you want. The output from stanford source will be a tab-delimited text file that you can load back into R. Hope that helps. Sean
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Peter ▴ 170
@peter-1556
Last seen 7.0 years ago
Sharon wrote: > And, another related question is: How can I use *getGEO() * with the > already downloaded GSE2718.soft.gz file (to avoid subsequent > downlaoding). Use the filename argument to getGEO to parse and existing file, rather than downloading it again. For example: library(Biobase) library(GEOquery) #Download GEO file, put it in the current directory, and load it: gse <- getGEO('GSE2718', destdir=".") #Or, open an existing GEO file (even if its compressed): gse <- getGEO(filename='GSE2718.soft.gz') Peter
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