Hello,
I am trying to do normalization the data of GSE8397 with MAS5.0 by using R:
setwd("D:/justforR/GSE8397")
source("http://bioconductor.org/biocLite.R")
biocLite()
library(affy)
affy.data = ReadAffy()
However, the data used to 2 platforms: Affymetrix Human Genome U133A and Affymetrix Human Genome U133B Array.
The code gave me the warning message: "Error in affyio::read_abatch(filenames, rm.mask, rm.outliers, rm.extra, :
Cel file D:/justforR/GSE8397/GSM208669.cel does not seem to be of HG-U133A type"
So, how can I keep normalizing the data when they are in both U133A and B? Should I try another method of normalization (RMA or GCRMA?)
DO you have any ideas about this problem?
Thank you so much!
Hi Phung,
I guess it's impossible to analyze these two types of affymetrix arrays by simple command lines. in fact U133A and U133B share only 168 probes among the 22k sondes in both designs. take a look at this post (https://www.biostars.org/p/283639/). in fact both designs are sold to be used as complementary and can't be compared.
fred
Hi Phụng Dương,
As Daniel C. Swan
suggested that we cannot combine these platform but there is other answer which might help you.https://www.biostars.org/p/287558/
You can analyze the sample seperately and then combine that is what it suggests. As many genes are still present in both the sample files.
I tried using some cell files of GSE8397 containing 2 data from 2 different platform.
mydata
- Badges
- Science topic
- Similar topics
- Correction