Question: CEL to Cibersort mix files, fails find Affymatrix specs
0
gravatar for thrabe
3.9 years ago by
thrabe0
United States
thrabe0 wrote:

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 • 1.2k views
ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by thrabe0
Answer: CEL to Cibersort mix files, fails find Affymatrix specs
0
gravatar for James W. MacDonald
3.9 years ago by
United States
James W. MacDonald51k wrote:

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.
 

ADD COMMENTlink written 3.9 years ago by James W. MacDonald51k
Answer: CEL to Cibersort mix files, fails find Affymatrix specs
0
gravatar for thrabe
3.9 years ago by
thrabe0
United States
thrabe0 wrote:

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

ADD COMMENTlink written 3.9 years ago by thrabe0
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