run OLIGO package encounters errors:
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83310199 • 0
@83310199-20052
Last seen 3.2 years ago

Hello everyone!

I used the oligo package to run the gene chip analysis and encountered a problem as follows:

I look forward to your reply, thank you!

source("https://bioconductor.org/biocLite.R")

setwd('D://R/affy/')

library(oligo)

data.dir <- 'D://R/affy/'

(celfiles <- list.files(data.dir, "\\.CEL$"))

data.raw <- read.celfiles(filenames = file.path(data.dir, celfiles))

treats <- strsplit("NT NT NT NT NT RCC RCC RCC RCC RCC", " ")[[1]]

(snames <- paste(treats, 1:5, sep = ""))

sampleNames(data.raw) <- snames

pData(data.raw)$index <- treats

sampleNames(data.raw)

pData(data.raw)

fit1 <- fitProbeLevelModel(data.raw)

boxplot(fit1, names = NA, col = as.factor(treats))

legend("topright", legend = unique(treats), fill = as.factor(unique(treats)),
       box.col = NA, bg = "white", inset = 0.01)

par(mfrow = c(2, 2))

MAplot(data.raw[, 1:10], pairs = FALSE)

data.eset <- rma(data.raw)

data.exprs <- exprs(data.eset)

str(data.exprs)

head(data.exprs)

xpa <- paCalls(data.raw)

> xpa <- paCalls(data.raw)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘paCalls’ for signature ‘"HTAFeatureSet"’
oligo • 344 views
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