I 'm trying to perform a DE analysis on CEL files. I've had to download the miRNA-4_0-st-v1.cdf file and to create a package using the
make.cdf.package function; then I tried to install it in the shell but I encountered the following error, even if I load the AnnotationDbi package in R :
R CMD INSTALL C:\Users\MM~1\AppData\Local\Temp\RtmpaURloF/mirna40cdf * installing to library 'C:/Program Files/R/R-4.0.2/library' ERROR: dependency 'AnnotationDbi' is not available for package 'mirna40cdf'
So I tried the
make.cdf.env function, but
ReadAffy doesn't work properly and gives me this error:
names <- dir(pattern = "*.CEL", path="~/cell/GSE143564_RAW",full.names = TRUE) d <- ReadAffy(filenames=names) AffyBatch object size of arrays=541x541 features (20 kb) cdf=miRNA-4_0 (??? affyids) number of samples=6 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain miRNA-4_0 Library - package mirna40cdf not installed Bioconductor - mirna40cdf not available Warning message:missing cdf environment! in show(AffyBatch)
How can I fix this? Here's the full code:
require(affy) library(makecdfenv) library(affxparser) convertCdf("miRNA-4_0-st-v1.cdf", "mirna40cdf", version=4, verbose=TRUE) pkgpath <- tempdir() make.cdf.package("mirna40cdf", version = packageDescription("makecdfenv", field = "Version"), species="Homo_sapiens", unlink=TRUE, compress=FALSE, package.path = pkgpath) mirna40cdf <- make.cdf.env("mirna40cdf") names <- dir(pattern = "*.CEL", path="~/cell/GSE143564_RAW",full.names = TRUE) d <- ReadAffy(filenames=names) d
I'm a very beginner and any advice is really appreciated. Thank you very much.