2 hours ago by
Republic of Ireland
Hi, you need to create the targets file yourself, or you can just create it as a data-frame within the R coding environment itself.
The metadata associated with each GEO record will usually have all information that you need. However, to give you an idea, your targets file for an Affymetrix study would look like:
FileName SampleID Group
SampleFiles/1_CS0911a_(HuGene-2_0-st).CEL CS0911a KN92
SampleFiles/10_CS0812d_(HuGene-2_0-st).CEL CS0812d KN92_WNT3A
SampleFiles/11_CS0812e_(HuGene-2_0-st).CEL CS0812e KN93_WNT3A
SampleFiles/12_CS0812f_(HuGene-2_0-st).CEL CS0812f KN93_WNT3A
SampleFiles/13_CS0801a_(HuGene-2_0-st).CEL CS0801a KN92
SampleFiles/14_CS0801b_(HuGene-2_0-st).CEL CS0801b KN92_WNT3A
SampleFiles/15_CS0801c_(HuGene-2_0-st).CEL CS0801c KN93_WNT3A
SampleFiles/16_CS1003a_(HuGene-2_0-st).CEL CS1003a KN92
SampleFiles/17_CS1003b_(HuGene-2_0-st).CEL CS1003b KN92
SampleFiles/18_CS1003c_(HuGene-2_0-st).CEL CS1003c KN92_WNT3A
SampleFiles/19_CS1003d_(HuGene-2_0-st).CEL CS1003d KN93_WNT3A
SampleFiles/2_CS0911b_(HuGene-2_0-st).CEL CS0911b KN92
SampleFiles/20_CS1003e_(HuGene-2_0-st).CEL CS1003e KN93_WNT3A
SampleFiles/3_CS0911c_(HuGene-2_0-st).CEL CS0911c KN92_WNT3A
SampleFiles/4_CS0911d_(HuGene-2_0-st).CEL CS0911d KN92_WNT3A
SampleFiles/5_CS0911e_(HuGene-2_0-st).CEL CS0911e KN93_WNT3A
SampleFiles/6_CS0911f_(HuGene-2_0-st).CEL CS0911f KN93_WNT3A
SampleFiles/7_CS0812a_(HuGene-2_0-st).CEL CS0812a KN92
SampleFiles/8_CS0812b_(HuGene-2_0-st).CEL CS0812b KN92
SampleFiles/9_CS0812c_(HuGene-2_0-st).CEL CS0812c KN92_WNT3A
I have not anonymised this data because these samples belong to a study of mine that is just accepted for publication (and that already has a GSE ID). I did not put the parentheses in the filenames.
You should be using the oligo package functions, by the way, something along the lines of:
library('limma')
library('oligo')
targetinfo <- readTargets('Targets.txt', sep = 't')
CELFiles <- list.celfiles('SampleFiles/', full.names = TRUE)
project <- read.celfiles(CELFiles)
# Background correct, normalize, and calculate gene expression
project.bgcorrect.norm.avg <- rma(project, background = TRUE, normalize = TRUE, target = 'core')
Nota Bene! - after you read in the data, please verify that the columns of project.bgcorrect.norm.avg perfectly align with whatever other metadata you are using.
Kevin
