"Error in ReadAffy() : could not find function "ReadAffy". Can any one please help how i can read :CEL file and perform rma.

Question

affy() can not read MoGene2_0-st.CEL file

0

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aacharya • 0

@aacharya-16535

Last seen 6.5 years ago

Hi I am running script to read the MoGene-2_0-st.CEL file but unfortunately the error is coming

"Error in ReadAffy() : could not find function "ReadAffy". Can any one please help how i can read :CEL file and perform rma.

#########CONSTRUCTING ESETs WITH .CEL FILES THROUGH AFFY###############
source("http://bioconductor.org/biocLite.R")
biocLite("affy")#Installs Affy i
library(affy)#Deploys Affy Package

setwd("C:/Users/akp0396//RTest cell file/Helene CEL file")#Define in folder
data<-ReadAffy()#Automatically reads the .CEL files present in the folder
data<-rma(data)

Error in ReadAffy() : could not find function "ReadAffy"

B-also I have tried by deploying "oligo" but then also i am getting error message which is as

oligo:::getCelChipType("C:/Users/akp0396//RTest cell file/Helene CEL file", TRUE)

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
namespace ‘BiocGenerics’ 0.26.0 is already loaded, but >= 0.27.1 is required

Thanks

Avi

microarray • 867 views

ADD COMMENT • link updated 6.5 years ago by James W. MacDonald 67k • written 6.5 years ago by aacharya • 0

score 2 · Answer 1 · 2018-07-24

2

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 7 hours ago

United States

You can't use the affy package to analyze those chips. Use oligo instead. And the error for part B of your question indicates that you have a problem with your Bioconductor installation. You should start R, then do

remove.packages("BiocInstaller")

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

biocLite(ask = FALSE)

After which things should work correctly.

ADD COMMENT • link 6.5 years ago James W. MacDonald 67k

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Entering edit mode

Dear James,

I did remove the packages and then I ran the scrip below but still the problem persist i cant bale to deploy oligo library. I cant able to understand what mistake I am doing :/-

############### GeneChip_Analysis.R#############
@@ -0,0 +1,105 @@
# basic libraries to load
library(oligo)
library(reshape)
library(ggplot2)
library(gridExtra)
library(limma)

# libraries based on the genechip
library(mogene20sttranscriptcluster.db)

# set working directory

########### load sample/phenotype data ################
s <- read.csv("/data/samples.csv") #usually contains the id, type/treat of sample
grps <- s$type # type of samples
names <- s$id # id of samples
########### load sample/phenotype data ################

################## get normalized counts #########################
setwd("C:/Users/akp0396/Desktop/R/Rui file/Test cell file/Helene CEL file")
(celFiles <- list.celfiles(getwd())) # get list of cel files
affyGeneFS <- read.celfiles(celFiles,verbose=TRUE) # read celFiles
con2 <- dbpd.mogene.2.0.st) # db connection
eset <- rma(affyGeneFS, target='core') # # rma normalization GeneFeatureSet
eset <- rma(affyGeneFS) # # rma normalization ExpressionFeatureSet

expr.unnorm <- exprs(affyGeneFS) # contains unnormalized counts of all genes
expr <- exprs(eset) #contains normalized counts of all genes
################## get normalized counts #########################

Error

> library("oligo", lib.loc="~/R/win-library/3.5")
Loading required package: oligoClasses
Error: package or namespace load failed for ‘oligoClasses’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
namespace ‘BiocGenerics’ 0.26.0 is already loaded, but >= 0.27.1 is required
Error: package ‘oligoClasses’ could not be loaded
> (celFiles <- list.celfiles(getwd())) # get list of cel files
[1] "1_Beuf_(MoGene-2_0-st).CEL" "10_Beuf_(MoGene-2_0-st).CEL" "11_Beuf_(MoGene-2_0-st).CEL" "12_Beuf_(MoGene-2_0-st)_2.CEL" "2_Beuf_(MoGene-2_0-st).CEL"
[6] "3_Beuf_(MoGene-2_0-st).CEL" "4_Beuf_(MoGene-2_0-st).CEL" "5_Beuf_(MoGene-2_0-st).CEL" "6_Beuf_(MoGene-2_0-st).CEL" "7_Beuf_(MoGene-2_0-st).CEL"
[11] "8_Beuf_(MoGene-2_0-st).CEL" "9_Beuf_(MoGene-2_0-st).CEL"
> affyGeneFS <- read.celfiles(celFiles,verbose=TRUE) # read celFiles
Error in read.celfiles(celFiles, verbose = TRUE) :
could not find function "read.celfiles"

##############

ADD REPLY • link 6.5 years ago aacharya • 0

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Entering edit mode

That error is implying that you have a devel version of oligoClasses mixed in with a release Bioconductor install. You should do

library(BiocInstaller)

biocValid()

and then do what it tells you.

ADD REPLY • link 6.5 years ago James W. MacDonald 67k