CEL to Cibersort mix files, fails find Affymatrix specs
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thrabe • 0
@thrabe-9205
Last seen 5.6 years ago
United States

Hi there, I have a problem with adding another chip specs. to my libraries. Based on the CEL -> Cibersort conversion script, I ran

source("http://bioconductor.org/biocLite.R")
biocLite("hthgu133pluspmprobe")

as root to install the chip specs, but when I run

source("http://bioconductor.org/biocLite.R")
library(affy) library(annotate)
library(hgu133plus2hsentrezgcdf)
library(org.Hs.eg.db)
library('hthgu133pluspmprobe')
allFiles <- list.files('./GSE45291',full.names=TRUE)
Data<-ReadAffy(filenames = allFiles[0:10],cdfname = "hthgu133pluspmprobe")
#eset<-rma(Data)
eset<-mas5(Data)

mas5 gives me

background correction: mas 
PM/MM correction : mas 
expression values: mas 
background correcting...
Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain hthgu133pluspmprobe
Library - package hthgu133pluspmprobecdf not installed
Bioconductor - hthgu133pluspmprobecdf not available​

 

What am I doing wrong? It worked before for some reason. Sorry, but I am relatively new to Bioconductor and R, I am a C++ person.

 

affy cel • 1.3k views
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@james-w-macdonald-5106
Last seen 9 hours ago
United States

Unless you are doing something particular you don't have to specify the cdf package. And the package with 'probe' in its name is not a cdf package (it's the one with 'cdf' in its name).

In addition, you might want to consider using rma() instead of mas5(). The RMA algorithm has been the de facto standard for well over a decade now, and MAS5.0 isn't even (to my knowledge) part of Affy's own software these days.
 

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Entering edit mode
thrabe • 0
@thrabe-9205
Last seen 5.6 years ago
United States

Hi James,

I am not sure what is happening. I run 

source("https://bioconductor.org/biocLite.R")
biocLite('hthgu133pluspmprobe')

in R to install the hthgu133pluspmprobe package, but when I load data and run rma, I get this:

library(hthgu133pluspmprobe)
allFiles <- list.files('./GSE45291',full.names=TRUE)
Data<-ReadAffy(filenames = allFiles[0:50],cdfname = "hthgu133pluspmprobe")#hgu133plus2hsentrezgcdf,hthgu133pluspmprobe
eset<-rma(Data)

Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain hthgu133pluspmprobe
Library - package hthgu133pluspmprobecdf not installed
Bioconductor - hthgu133pluspmprobecdf not available

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