search for: geoquery

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 host" Como no podía cargar los datos directamente, me descargué el archivo y al intentarlo cargar desde el orde...

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 de...

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

...3: package 'Biostrings' was built under R version 2.9.0 and help may not work correctly 4: package 'IRanges' was built under R version 2.9.0 and help may not work correctly 5: package 'CORNA' was built under R version 2.9.0 and help may not work correctly 6: package 'GEOquery' was built under R version 2.9.0 and help may not work correctly 7: package 'microRNA' was built under R version 2.9.0 and help may not work correctly 8: package 'Rlibstree' was built under R version 2.9.0 and help may not work correctly > I am stuck. Which packages am I...

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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...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: https://stat.ethz.ch/pipermail/bioconductor/2007-August/018947.html (the relevant command is library(GEOquery); gse <- getGEO('GSE94')) https://stat.ethz.ch/pipermail/bioconductor/2007-July/018204.html I think solutions are: * Specify the encoding in readLines. * Convert the input using iconv. * Tell the user to set their locale to match the input file (!) Unfortunately, these (1 & 2,...

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 ÊÔ¿ªURL'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/by_series/GSE3524/GSE3524_family.soft.gz' ftp data connection made, file length 3586385 bytes ´ò¿ªÁËURL downloaded 3502Kb File stored at...

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