Question: how to read MoGene-2_0-st.CEL files
0
gravatar for aacharya
9 months ago by
aacharya10
Germany
aacharya10 wrote:

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
R gene • 533 views
ADD COMMENTlink modified 9 months ago by finswimmer11k • written 9 months ago by aacharya10

Hello and welcome aacharya,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

Thank you!

fin swimmer

ADD REPLYlink written 9 months ago by finswimmer11k

Hello fin swimmer,

The tip is really helpful :)

Best Regards Avi

ADD REPLYlink written 9 months ago by aacharya10

Which R version are you using?; What happened after you ran library(affy)? Also note the error on BiocGenerics

I am using R version 3.5.1 (2018-07-02) -- "Feather Spray". BiocGenerics is loaded with affy:

require(affy)
Carregando pacotes exigidos: affy
Carregando pacotes exigidos: BiocGenerics
Carregando pacotes exigidos: parallel
ADD REPLYlink modified 9 months ago • written 9 months ago by Kevin Blighe41k

Hello aacharya!

It appears that your post has been cross-posted to another site: Cross-posted at https://support.bioconductor.org/p/111334/

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 9 months ago by Kevin Blighe41k

Hi Kevin, I am a new user and I am learning so expect experts like you may handle with experience :) while ran the library(affy) I am getting the Error ReadAffy() : could not find function "ReadAffy" I am still searching appropriate scripts to read and perform rma.

Thanks for your support

Regards Avi

ADD REPLYlink written 9 months ago by aacharya10

Did you try the solution by James on Bioconductor? - https://support.bioconductor.org/p/111334/#111377

ADD REPLYlink written 9 months ago by Kevin Blighe41k
1

Yes! but unfortunately after performing that, the problem didn't solve . so I removed 'oligo' and I reinstall library(oligo) with packages("Rcpp") then after that I can able read and perform the RMA.

Thanks for all the information and support :)

Best Regards Aviseka

ADD REPLYlink written 9 months ago by aacharya10
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