search for: geoqueri

Hola, buenas tardes, Hace unos dias que intento cargar unos datos de microarrays del ncbi con versión de R 2.15.2 de 32 bits en windows xp. he utilizado el siguiente codigo: library(Biobase) library(GEOquery) library(limma) gset <- getGEO("GSE6536", GSEMatrix =TRUE) Al hacerlo me da este error: "Error in function (type, msg, asError = TRUE) : couldn't connect to

Hi all, I am trying to install the package "GEOquery" in unix. I have downloaded the standard version of R and this package is not contained in the default. I know that I can select repositories under windows but I don't know how to do it in unix. Does anyone have any idea on this? Thank you in advance, Eleni [[alternative HTML version deleted]]

So, I''m working on a search engine of sorts that restricts results to your local area. I can successfully return all entries within 15 miles of a particular point, and I can successfully return all entries that match a search query, but I''m having trouble combining the two together and doing pagination on them. Basically, for the range query, you do a SQL query that returns all

I recently updated R 2.10.1 Patched (2010-02-20 r51163) This morning I reinstalled biomaRt using biocLite. Now I can no more connect to biomaRt and even the following instruction is hanging for a while until the same error message pops up. > listMarts() Error in value[[3L]](cond) : Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the

Dear R-ers, I am using getGEO to download expression data from the Gene Expression Omnibus. With default settings, when a file is downloaded and parsed, lots of dotted lines are printed in the terminal, like this: .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... ..........

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R-developers, I'm looking for some 'best practices', or perhaps an upstream solution (I have a deja vu about this, so sorry if it's already been asked). Problems occur when a file is encoded as latin1, but the user has a UTF-8 locale (or I guess more generally when the input locale does not match R's). Here are two examples from the Bioconductor help list:

Hi, all I met a problem to query GSE3524, which cannot be open on my computer. I hope some of you would be kind to give me some advice. Thanks! The code is as follow: ################## library(GEOquery) gsename="GSE3524" gse=getGEO(gsename) ################## The error information follows as

I have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is