This is the first time I've ever posted on biostars, and I'm still not 100% sure of the etiquette - please feel free to berate me if I've forgotten to mention something as I'm here to learn.
I've been trying to understand this problem for the best part of 3 days now, and would like some help.
I've been given a number of CEL files that were produced using a GeneChip™ miRNA 4.0 Array. The samples have come from human tissue. In an attempt to obtain the expression data, I have written the following R script:
library(oligo) # I've seen some issues with this failing to load on oligo::read.celfiles. library(pd.mirna.4.0) celFiles <- oligoClasses::list.celfiles("/home/uid/path/to/data", full.names=TRUE) rawData <- oligo::read.celfiles(celFiles) expressionSet <- oligo::rma(rawData)
This returns a "Large ExpressionSet" of 2.5Mb in size (from the original 17.9Mb loaded in as rawData). Sadly, when I want to take a look at the probe identifiers, only control probes seem to be returned (as in everything ending with "_st").
I'm not 100% sure where I've gone wrong here as I've analysed quite a lot of miRNA in the past - although this is my first attempt at analysing GeneChip miRNA 4.0 Array data.
Any help would be massively appreciated.