Question: Same code for different versions of the same platform
0
gravatar for Joe Kherery
7 months ago by
Joe Kherery30
Joe Kherery30 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 • 183 views
ADD COMMENTlink modified 7 months ago • written 7 months ago by Joe Kherery30
1

Try it and find out.

ADD REPLYlink written 7 months ago by YaGalbi1.4k

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 7 months ago by Joe Kherery30

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

ADD REPLYlink written 7 months ago by Alex Reynolds26k

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

ADD REPLYlink written 7 months ago by Joe Kherery30

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 7 months ago • written 7 months ago by Alex Reynolds26k
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