Agilent array in R

Agilent array in R

0

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)


colour


two


microarray


problems

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