Hi everyone, I am analyzing the GSE7329 dataset and download .txt raw data. I used this code However, when it comes to the QA steps including image and boxplot, I get this errors
`require('limma')
targetinfo <- readTargets('targets.txt', sep = '\t')
project <- read.maimages(targetinfo, source = 'agilent')
# Perform background correction on the fluorescent intensities
project.bgcorrect <- backgroundCorrect(project, method = 'normexp', offset = 16)
# Normalize the data with the 'loess' method
project.bgcorrect.norm <- normalizeWithinArrays(project.bgcorrect, method = 'loess')
project.bgcorrect.norm.avg <- avereps(
project.bgcorrect.norm,
ID = project.bgcorrect.norm$genes$ProbeName)
boxplot(
project.bgcorrect.norm.avg,
col = "royalblue",
las = 2)`
Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) : 'x' must be atomic
# Generate chip images to diagnose spatial artifacts
image(project)
Error in image.default(project) : 'z' must be a matrix
2- Based on LIMMA package, MA list has M and A which are log ratio and average log ratio, can I use one of them as the expression matrix for further analysis and QA?
3- for an expression matrix from MAList as when I used exprs.MA, the matrix had two columns for each array but I do not know how to deal with it, should I average them?
4- I also read in the limma package, there is a separate analysis when there is a common reference, in the paper of this data they only used part of the samples as a target reference as cy3 here is it
"We also made reference target by using pooled total RNA from the 14 individuals for reference and labeled it with Cy3 fluorescence."
Can I proceed with this code as targets.txt did not specify anything regarding the reference target, here is the targets.txt contents
> show(targets)
FileName disease
1 SampleFiles/GSM176570.txt FX
2 SampleFiles/GSM176575.txt FX
3 SampleFiles/GSM176579.txt FX
4 SampleFiles/GSM176583.txt FX
5 SampleFiles/GSM176586.txt C
6 SampleFiles/GSM176589.txt C
