HuGene-1_1-st accessory files for microarray analysis
1
0
Entering edit mode
7.3 years ago
themantalope ▴ 40

Hi All,

I'm trying to analyze the data from this GEO repository with XPS and limma in R. I was able to get the probeset and transcript csv files from the Affymetrix website, but it looks like I also need two other files, a clf file and a pgf file. I'm not sure where to get these files, as I don't see anything from Affymetrix. Is it possible to create these files?

microarray affymetrix • 2.1k views
ADD COMMENT
0
Entering edit mode
7.2 years ago

Hey,

Download the raw data CEL files and use the oligo and limma packages to process these. I do not believe you need any other files other than these [CEL files].

Here is how I processed similar arrays (your CEL files will be located in a directory called SampleFiles/):

source("http://bioconductor.org/biocLite.R")
require("limma")
#'oligo' is more suited for the Gene ST Affymetrix arrays
require("oligo")

#Disable scientific notation
options(scipen=999)

targetinfo <- readTargets("Targets.txt", sep="\t")
CELFiles <- list.celfiles("SampleFiles/", full.names = TRUE)

#Raw intensity data
project <- read.celfiles(CELFiles)

#Background correct, normalize, and calculate gene expression
project.bgcorrect.norm.avg <- rma(project, background=TRUE, normalize=TRUE, target="core")
project.bgcorrect.norm.avg.Exons <- rma(project, background=TRUE, normalize=TRUE, target="probeset")

#Perform some diagnostics on the arrays
#Generate chip images to diagnose spatial artifacts for each array and a merged boxplot of intensities
pdf("Output/ChipImageQC.pdf")
    image(project)
dev.off()
pdf("Output/BoxPlotQC.pdf")
    par(mar=c(5,5,5,5), cex=1, cex.axis=0.8, mfrow=c(2,1))

    boxplot(project, which="all", transfo=log2, main="Raw chip fluorescent intensities", names=samplenames, las=2)
    boxplot(project.bgcorrect.norm.avg, transfo=log2, main="Background-corrected, RMA normalised, log2 expression values\nAll probes", names=samplenames, las=2)
dev.off()


#Write out the normalised expression values
write.table(project.bgcorrect.norm.avg, "NormalisedCounts.GeneSummarised.tsv", sep="\t", quote=FALSE)
write.table(project.bgcorrect.norm.avg.Exons, "NormalisedCounts.ExonSummarised.tsv", sep="\t", quote=FALSE)
ADD COMMENT
0
Entering edit mode

For annotation, see the working example here: A: Affymetrix Human Genome U133 Plus 2.0 Array

Also see the biomaRt vignette (section 4.1).

ADD REPLY

Login before adding your answer.

Traffic: 2000 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6