simpleaffy with hgu133plus2
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dorothyc ▴ 140
@dorothyc-3150
Last seen 7.1 years ago
Hi, I'm trying to do simpleaffy pairwise comparison on hgu133plus2 data. However, I'm running into problems with results.summary() (please see below). It didn't recognize hgu133plus2 because the package now is called hgu133plus2.db. But when I assigned "hgu133plus2.db" to "arrayid", I got another error. -------------- >require(hgu133plus2.db) >require(simpleaffy, quietly = TRUE) >covdesc <- "covdesc.txt" >arrayid <<- "hgu133plus2" >raw.data <- read.affy(covdesc = covdesc) >eset <<- rma(raw.data) >x.results <- pairwise.comparison(eset, names(pData(raw.data)) [groupcol], spots=raw.data, method="unlogged", logged=TRUE) options(warn = -1) >x.summary <- results.summary(x.results, arrayid) Error in library(cdfname, character.only = TRUE) : there is no package called 'hgu133plus2' > arrayid <- "hgu133plus2.db" > x.summary <- results.summary(x.results, arrayid) Error in get(paste(cdfname, "SYMBOL", sep = "")) : variable "hgu133plus2.dbSYMBOL" was not found ---------- Your insight is very much appreciated. Thanks in advance. Regards, Dorothy [[alternative HTML version deleted]]
hgu133plus2 simpleaffy hgu133plus2 simpleaffy • 643 views
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