Question: HuGene-1_1-st accessory files for microarray analysis
0
gravatar for themantalope
17 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 • 693 views
ADD COMMENTlink modified 15 months ago by Kevin Blighe35k • written 17 months ago by themantalope40
0
gravatar for Kevin Blighe
15 months ago by
Kevin Blighe35k
Republic of Ireland
Kevin Blighe35k 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 5 months ago • written 15 months ago by Kevin Blighe35k

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 5 months ago by Kevin Blighe35k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1720 users visited in the last hour