Agilent array in R
1
0
Entering edit mode
6 weeks ago
Monika • 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 • 211 views
ADD COMMENT
0
Entering edit mode
5 weeks ago

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

ADD COMMENT

Login before adding your answer.

Traffic: 2437 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6