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CSB-IG / rnw

regulation network workflow
GNU General Public License v3.0
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Auto downloader from GEO #2

Open hachepunto opened 9 years ago

hachepunto commented 9 years ago

Escribir el programa para autodowloader los CEL files (GSM) o bien los conjuntos de CEL files (GSE)

Sería conveniente que checara repetidos (usar checksum)

Comando que podría servir para bajar los GSM:

wget --ignore-case ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM272nnn/GSM272727/suppl/GSM272727*.CEL.gz

rgarcia-herrera commented 9 years ago

Hay un API de python para usar el omnibus: http://pythonhosted.org/Orange-Bioinformatics/reference/geo.html

rgarcia-herrera commented 9 years ago 
# Version info: R 2.14.1, Biobase 2.15.3, GEOquery 2.23.2, limma 3.10.1
# R scripts generated  Wed Jun 3 12:01:47 EDT 2015

# Unable to generate script analyzing differential expression.
#      Invalid input: at least two groups of samples should be selected.

################################################################
#   Boxplot for selected GEO samples
library(Biobase)
library(GEOquery)

# load series and platform data from GEO

gset <- getGEO("GSE53394", GSEMatrix =TRUE)
if (length(gset) > 1) idx <- grep("GPL96", attr(gset, "names")) else idx <- 1
gset <- gset[[idx]]

# set parameters and draw the plot

dev.new(width=4+dim(gset)[[2]]/5, height=6)
par(mar=c(2+round(max(nchar(sampleNames(gset)))/2),4,2,1))
title <- paste ("GSE53394", '/', annotation(gset), " selected samples", sep ='')
boxplot(exprs(gset), boxwex=0.7, notch=T, main=title, outline=FALSE, las=2)
legend("topleft", labels, fill=palette(), bty="n")