Question: Same code for different versions of the same platform
0
gravatar for Joe Kherery
2.4 years ago by
Joe Kherery100
Joe Kherery100 wrote:

I would like to use the R code that I wrote to analyze affymetrix human genome u133 plus 2.0 array to analyze Affymetrix Human Genome U219

I would like to know if I can use the same code for different versions of the same platform;

library(simpleaffy)
celfiles <- read.affy(covdesc="phenodata.txt")
celfiles.rma <- rma(celfiles)
samples <- celfiles.rma$Target
samples
samples <- as.factor(samples)
design <- model.matrix(~0 + samples)
colnames(design) <- c("control","disease")
library(limma)
fit <- lmFit(exprs(celfiles.rma), design)
contrast.matrix <- makeContrasts(disease-control, levels=design) 
fit.con <- contrasts.fit(fit, contrast.matrix)
fit.eb <- eBayes(fit.con)
probeset.list <- topTable(fit.eb, coef=1, number=50000, adjust.method="BH", lfc=1.5)
microarray R • 476 views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Joe Kherery100
1

Try it and find out.

ADD REPLYlink written 2.4 years ago by YaGalbi1.5k

Dear YaGalbi, OFC I tried this before posting here. And yes it worked, but I'm not sure if there's something missing from the code that is needed in another version of the same platform.

ADD REPLYlink written 2.4 years ago by Joe Kherery100

Don't they publish a manifest or other document schema for each release? That would help confirm or disprove fears.

ADD REPLYlink written 2.4 years ago by Alex Reynolds30k

Dear, Alex Reynolds They did not publish supplementals to compare.

ADD REPLYlink written 2.4 years ago by Joe Kherery100

I'm surprised there is no schema for the documents they put out. Especially from a commercial entity. If things don't work, I guess all you can do is try to reverse-engineer the data format.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Alex Reynolds30k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 716 users visited in the last hour