arrayanalysis.org custom CDF version

Question

[tleona3]

Hi all,

I'm using this on-line module to do the pre-processing and QC of my .CEL microarray data. My question is quite simple, but I after looking through their documentation I cannot find an answer.

When mapping to a custom CDF (say hgu133plus2_Hs_ENSG), how can I know which brain array version of this it is mapping to? If anyone knows whether it is the most updated version of the brain array custom CDFs or if it is a specific one that would be great! The link to their website/documentation is below. Thanks so much.

arrayanalysis.org/documentation

[Kevin Blighe]

Hey, I would hope that the program you are using produces a log file of some sort, in which it should state the exact CDF version being used...?

[tleona3]

Thanks Kevin, I ended up just doing it using Affy once I downloaded the specific custom CDF I wanted to use from Brain Array. For those who may have issues installing and applying the custom CDF, I've posted my script below.

    #Set working directory

setwd("~/Desktop/mc")

#Install Custom CDF package based on brain array file you downloaded

install.packages("~/Desktop/mc/mouse4302mmensgcdf_22.0.0.tar.gz", repos = NULL, type = "source")

#Load affy package

library(affy)

#Load custom CDF package

library("mouse4302.db", lib.loc="/Library/Frameworks/R.framework/Versions/3.4/Resources/library")

#Create affybatch using custom CDF, first tell R where the .CEL files are

cels = list.files("~/Desktop/mc", pattern = ".CEL")

Data=ReadAffy(verbose=TRUE, filenames=cels, cdfname="mouse4302mmensgcdf")

#Run Affy RMA

Data.RMA=rma(Data)