Tutorial:How To Install A Specific Cdf Package For Use In Bioconductor
0
20
Entering edit mode
8.3 years ago

Sometimes you may wish to use a CDF file obtained from somewhere (besides the default ones provided through BioConductor). This tutorial is not about how to make such a CDF. But, merely about how to install it and use it with existing Bioconductor packages such as affy and rma.

#Create a package for downloaded CDF
#This assumes you have already downloaded or created a CDF and you just want to use it in Bioconductor with (for example) ReadAffy
#For example suppose you wanted to use a specific CDF from the Affy web site:
#http://www.affymetrix.com/support/technical/byproduct.affx?product=hugene-1_0-st-v1

#Note, this example is purely for illustration. There is no real need to create a package for HuGene-1_0-st-v1
#This chip is already supported by BioConductor and can be loaded with 
#library(hugene10stv1cdf)   #cdfname="hugene10stv1"

#Install package for making cdf packages
source("http://bioconductor.org/biocLite.R")
biocLite("makecdfenv")
library(makecdfenv)

#Create CDF package in temporary directory 
pkgpath <- tempdir()
make.cdf.package("HuGene-1_0-st-v1.r3.cdf", cdf.path="/Users/ogriffit/Downloads/HuGene-1_0-st-v1.r3.unsupported-cdf", compress=FALSE, species = "Homo_sapiens", package.path = pkgpath)
dir(pkgpath)

#Install that package at a terminal using 'pkgpath' from above
#R CMD INSTALL /var/folders/8j/bqry255x52q6_dhyw22w6sq80000gn/T//Rtmppd9YEK/hugene10stv1.r3cdf

#Then, load it for use here
library(hugene10stv1.r3cdf)

#Download a CEL file package for testing purposes
getGEOSuppFiles("GSE27447")

#Unpack the CEL files
untar("GSE27447/GSE27447_RAW.tar", exdir="data")
cels = list.files("data/", pattern = "CEL")
sapply(paste("data", cels, sep="/"), gunzip)
cels = list.files("data/", pattern = "CEL")

setwd("/Users/ogriffit/data")
raw.data=ReadAffy(verbose=TRUE, filenames=cels, cdfname="hugene10stv1.r3cdf") #Custom installed CDF

#You can now go on to whatever normalizing and analysis you wish with the data using your custom CDF package
#perform RMA normalization 
data.rma.norm=rma(raw.data)

#Get the important stuff out of the data - the expression estimates for each array
rma=exprs(data.rma.norm)
bioconductor affymetrix tutorial Tutorial • 12k views
ADD COMMENT
0
Entering edit mode

I think one more bioconductor package that also needs to be installed is `s4vector` http://www.bioconductor.org/packages/release/bioc/html/S4Vectors.html

ADD REPLY
0
Entering edit mode

i was trying to add this to comment instead #quickfingers.

ADD REPLY
0
Entering edit mode

Hi,

I tried to follow the example using the file GPL8715_Hs133P_Hs_UG_8.cdf. But when I try to normalize using the rma method, I get the next error:

Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain GPL8715Hs133PHsUG8cdf Library - package gpl8715hs133phsug8cdf not installed Bioconductor - gpl8715hs133phsug8cdf not available In addition: Warning message: missing cdf environment! in show(AffyBatch)

In the previous steps, I dind't get any error message and I can load the new created package even.

How can I fix it?

Best regards,

Juan.

ADD REPLY
0
Entering edit mode

Start by opening a new post with your question. Please do not use the ANSWER box to ask questions.

ADD REPLY

Login before adding your answer.

Traffic: 1849 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6