Question: HuGene-1_1-st accessory files for microarray analysis
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gravatar for themantalope
14 months ago by
themantalope40
themantalope40 wrote:

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?

affymetrix microarray • 611 views
ADD COMMENTlink modified 13 months ago by Kevin Blighe30k • written 14 months ago by themantalope40
0
gravatar for Kevin Blighe
13 months ago by
Kevin Blighe30k
Kevin Blighe30k wrote:

Hey,

I have analysed the same microarray and had no issues using the oligo and limma packages. I do not believe that you need any other files other than the TSV files that you've already got. Here is how I processed the arrays:

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 COMMENTlink modified 3 months ago • written 13 months ago by Kevin Blighe30k

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 REPLYlink written 3 months ago by Kevin Blighe30k
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