Hi, I am using quite a lot the GEOquery libray. Recently I found out that the link to the GSE repository changed on GEO therefore the getGEOfile function fails to download the file.Since there is not the possibility to change the download path in the getGEOfile it will be nice if the mantainers of GEOquery could add a parameter to the function to allow it. Therefore, actually I am downloading locally the GSEXXX_family.soft.gz and I use the parseGEO function to reformat the GSE data. Yesterday, I tryed to parse the GSE3294_family.soft.gz: library(GEOquery) gse3294<-parseGEO("GSE3294_family.soft.gz") since after few hours nothing came out. I debugged the function and find out that the function freeze at the first line. first.entity <- findFirstEntity(con) The problem was encoutered with GEOquery 1.6.0, running Bioconductor 1.8 on windowXP centrino 2GHz, 1.5GB RAM on the GSE3294 Cheers Raf -- ---------------------------------------- Prof. Raffaele A. Calogero Bioinformatics and Genomics Unit Dipartimento di Scienze Cliniche e Biologiche c/o Az. Ospedaliera S. Luigi Regione Gonzole 10, Orbassano 10043 Torino tel. ++39 0116705420 Lab. ++39 0116705408 Fax ++39 0119038639 Mobile ++39 3333827080 email: raffaele.calogero at unito.it raffaele[dot]calogero[at]gmail[dot]com www: www.bioinformatica.unito.it

rcaloger wrote: > Hi, > I am using quite a lot the GEOquery libray. > Recently I found out that the link to the GSE repository changed on GEO > therefore the getGEOfile function fails to download the file.Since there > is not the possibility to change the download path in the getGEOfile it > will be nice if the mantainers of GEOquery could add a parameter to the > function to allow it. > > Raf, I'm glad to hear that you find GEOquery useful. I should probably add a URL parameter at some point, yes. However, in the short term, simply updating to the version 1.7.3 of GEOquery fixes the GEO URL issue. > Therefore, actually I am downloading locally the GSEXXX_family.soft.gz > and I use the parseGEO function to reformat the GSE data. > Yesterday, I tryed to parse the GSE3294_family.soft.gz: > library(GEOquery) > gse3294<-parseGEO("GSE3294_family.soft.gz") > parseGEO doesn't take a filename, but instead takes a connection. However, parseGEO probably isn't the best way to go about this if you have the .tar.gz file stored locally. getGEO() has a filename parameter, so you can simply do: gse3294 <- getGEO(filename='GSE3294_family.soft.gz') > since after few hours nothing came out. I debugged the function and find out that > the function freeze at the first line. first.entity <- findFirstEntity(con) > > This isn't a bug. As I mentioned above, parseGEO doesn't work this way and really isn't meant to be called by the end user (as mentioned in the help). > The problem was encoutered with GEOquery 1.6.0, running Bioconductor 1.8 on > windowXP centrino 2GHz, 1.5GB RAM on the GSE3294 > Thanks for including the GEOquery version and BioC version. Yes, you should upgrade your GEOquery package--biocLite() will do the trick. Let me know if you have more questions or if upgrading doesn't fix the problem. Sean