Hello all,
I need to compare the performance of RMA to mas5.0 normalization on some microarray data. This is not a matter of weighing the merits of rma against those of mas5, but rather seeing if a signal detected in rma normalized data is present when a different normalization technique, mas5.0, is carried out.
I used readAffy() to combine data from my .cel files:
> B_miRNA_wholechip_2outlrem <-affy::ReadAffy(filenames = "VV54m.CEL",
"VV51m.CEL",
"VV50m.CEL",
....)
Attempting to run mas5() on this gives the following error:
> B_miRNA_wholechip_2outlrem_mas5.0norm <- mas5(B_miRNA_wholechip_2outlrem, normalize = TRUE)
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 miRNA-4_0
Library - package mirna40cdf not installed
Bioconductor - mirna40cdf not available
So I TRIED to create the required package from the .cdf file on the affy page http://www.affymetrix.com/support/technical/byproduct.affx?product=miRNAGalaxy
> makecdfenv::make.cdf.package("miRNA-4_0-st-v1.cdf", species="human", package.path ="/Users/mylapple/Desktop/r_proj2/r_proj2_mRNA/sva")
Reading CDF file.
Creating CDF environment
Wait for about 251 dots...................................................................................................................................................................................................................................................
Creating package in /Users/mylapple/Desktop/r_proj2/r_proj2_mRNA/sva/mirna40stv1cdf
README PLEASE:
A source package has now been produced in
/Users/myapple/Desktop/r_proj2/r_proj2_mRNA/sva/mirna40stv1cdf.
Before using this package it must be installed via 'R CMD INSTALL'
at a terminal prompt (or DOS command shell).
If you are using Windows, you will need to get set up to install packages.
See the 'R Installation and Administration' manual, specifically
Section 6 'Add-on Packages' as well as 'Appendix E: The Windows Toolset'
for more information.
Alternatively, you could use make.cdf.env(), which will not require you to install a package.
However, this environment will only persist for the current R session
unless you save() it.
Sure enough there is a folder named 'mirna40stv1cdf' was created by this process in my current working directory. In a terminal, from this working directory I run the command 'R CMD INSTALL'
$ R CMD INSTALL mirna40stv1cdf
installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘mirna40stv1cdf’ ...
etc.
Great. So I go back into R and try to make use of this:
> install.packages("mirna40stv1cdf")
> library(mirna40stv1cdf)
Attaching package: ‘mirna40stv1cdf’
The following objects are masked from ‘package:hgu133a2cdf’:
i2xy, xy2i
Go to run mas5 and...
> B_miRNA_wholechip_2outlrem_mas5.0norm <- mas5(B_miRNA_wholechip_2outlrem, normalize = TRUE)
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 miRNA-4_0
Library - package mirna40cdf not installed
Bioconductor - mirna40cdf not available
So it looks like what I downloaded from affy and created a package with gives me some library named "mirna40stv1cdf". Unfortunately what the mas5 function seems to be looking for is "mirna40cdf". I have found no separate file to download for "mirna40cdf". This zipped up .cdf file stuff from the affy site is all I can find. Googling "library mirna40cdf" or "package mirna40cdf" only turns up old forum posts by users struggling with the same problem (I have used these to inform what I did here) but nothing that seems to get me "mirna40cdf".
mirna40stv1cdf =/= mirna40cdf, I guess.
So what have I done wrong? How can I fix this? Where do I get "mirna40cdf"? I will note that trying to load the library(mirna40cdf) or install.packages("mirna40cdf") does nothing. I am fresh out of ideas.
Any help would be greatly appreciated.
