Biostar Beta. Not for public use.
Same code for different versions of the same platform
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2.2 years ago
Joe Kherery • 60

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)
R microarray • 291 views
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Try it and find out.

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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.

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

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

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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.

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