bioconductor

Installing a local package that's not a .tar.gz

Hey Fellow Rstaters, I'm working on a script that creates a package in the current directory (using pdInfoBuilder from BioConductor), and I'd like to install it while the script is running. install.packages() with repo=NULL seems like an obvious choice, but this seems to only except package directories tarballed and gzipped. Is there a ...

R statistical package: wrapping GOFrame objects

Dear all, I'm trying to generate GOFrame objects to generate a gene ontology mapping in R for unsupported organisms (see http://www.bioconductor.org/packages/release/bioc/vignettes/GOstats/inst/doc/GOstatsForUnsupportedOrganisms.pdf). However, following the instructions literally doesn't help me. Here's the code I execute (R 2.9.2 on u...

multiFASTA file processing

Hi all, I was curious to know if there is any bioinformatics tool out there able to process a multiFASTA file giving me infos like number of sequences, length, nucleotide/aminoacid content, etc. and maybe automatically draw descriptive plots. Also an R BIoconductor solution or a BioPerl module would do, but I didn't manage to find anyth...

R error allocMatrix

HI all, I was trying to load a certain amount of Affymetrix CEL files, with the standard BioConductor command (R 2.8.1 on 64 bit linux, 72 GB of RAM) abatch<-ReadAffy() But I keep getting this message: Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData, : allocMatrix: too many elements specified What's th...

In R, how do I set an S4 class based on another object's class

I need to create an object of type ShortReadQ from Bioconductor's ShortRead library. ShortReadQ 'signature(sread = "DNAStringSet", quality = "QualityScore", id = "BStringSet")' The quality slot needs to be an object inheriting from QualityScore, of which I can easily determine from another ShortReadQ object that I wish to em...

rpy2: Converting a data.frame to a numpy array

I have a data.frame in R. It contains a lot of data : gene expression levels from many (125) arrays. I'd like the data in Python, due mostly to my incompetence in R and the fact that this was supposed to be a 30 minute job. I would like the following code to work. To understand this code, know that the variable path contains the full pa...

R + Bioconductor : combining probesets in an ExpressionSet

Hi, First off, this may be the wrong Forum for this question, as it's pretty darn R+Bioconductor specific. Here's what I have: library('GEOquery') GDS = getGEO('GDS785') cd4T = GDS2eSet(GDS) cd4T <- cd4T[!fData(cd4T)$symbol == "",] Now cd4T is an ExpressionSet object which wraps a big matrix with 19794 rows (probesets) and 15 columns...