Question: Illumina BeadChip Array probe file Vs control probe file
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gravatar for nazaninhoseinkhan
12 months ago by
Iran, Islamic Republic Of
nazaninhoseinkhan360 wrote:

Hi every body,

I want to get the list of differential expressed genes from an Illumina BeadChip Array data set (Gse22155).

In Limma manual it has been said that BeadStudio is usually produced probe intensity file as well as control probe file which the latter is used for background correction and normalization.

However most data sets that I want to use, including gse22155, does not have control probe file.

Can anyone guide me how to analyze these types of Illumina BeadChip Arrays?

Thank u in advance

Nazanin

ADD COMMENTlink modified 9 months ago by Biostar ♦♦ 20 • written 12 months ago by nazaninhoseinkhan360

The data is already normalised; thus, the control probe information has already been utilised and is not provided.

library(Biobase)
library(GEOquery)

# load series and platform data from GEO

gset <- getGEO("GSE22155", GSEMatrix =TRUE, getGPL=FALSE)
if (length(gset) > 1) idx <- grep("GPL6947", 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 ("GSE22155", '/', annotation(gset), " selected samples", sep ='')
boxplot(exprs(gset), boxwex=0.7, notch=T, main=title, outline=FALSE, las=2)

d


Please confirm the exact data that you downloaded.

Kevin

ADD REPLYlink modified 12 months ago • written 12 months ago by Kevin Blighe41k

Thank u so much for your help Kevin

ADD REPLYlink written 12 months ago by nazaninhoseinkhan360
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