Agilent array in R

Question

[Monika]

Hi, I am doing two colour agilent array in R. I followed the script but... At one stage: project is RGList so this is correct but upon putting >

mage(project) Error in image.default(project) : 'z' musi być macierzą ("z needs to be matrix)

So i decided to do project == as.matrix(project) So then the project is matrix but the distinction between green and red is gone and everything is orange... how should i fix this?

targets <- readTargets('Targets.txt', sep = '\t')
getwd()
# Converts the data to a RGList (two-colour [red-green] array), with values for R, Rg, G, Gb
project <- read.maimages(targets, 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')

# For replicate probes in each sample, replace values with the average
project.bgcorrect.norm.avg <- avereps(
  project.bgcorrect.norm,
  ID = project.bgcorrect.norm$genes$ProbeName)





##QUALITY CONTROL


# Generate chip images to diagnose spatial artefacts
library(limma)


project <- as.matrix(project) ------> here is when i converted to matrix and everything is screwed up :(
project
image(project)
image(project.bgcorrect.norm.avg)

Answer 1

[Kevin Blighe]

You are following this for your [assumed] 2-colour Agilent array data: build the expression matrix step by step from GEO raw data

Please show the output of:

project
str(project)
project.bgcorrect.norm.avg
str(project.bgcorrect.norm.avg)

Kevin