GeneChip miRNA 4.0 processing in R - annotation data
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Entering edit mode
7.3 years ago
Jana • 0

Hello everyone,

I have been trying to create a package with annotation data for GeneChip miRNA 4.0 Array. Affymetrix people provided me with miRNA-4_0-st-v1.cdf and I created a annotation package using makecdfenv and affxparser. Using this package, I was able to read CEL files correctly, but then no subsequent processing is possible, as some data seems to be missing. Below I show one example for the error message I get. Do you have any idea, what needs to be done here? I couldn't find information in respective vignettes.

My code:


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="", unlink=TRUE, compress=FALSE, package.path = pkgpath)

##package installation from DOS shell (R CMD INSTALL "path to package")

library(mirna40cdf)
library(affy)

myData = ReadAffy()    
myData            

AffyBatch object
size of arrays=541x541 features (18 kb)
cdf=miRNA-4_0 (36249 affyids)
number of samples=4
number of genes=36249
annotation=mirna40
notes=

library(simpleaffy)
myQC = qc(myData)

Error in setQCEnvironment(cdfn) : 
Could not find array definition file ' mirna40cdf.qcdef '. Simpleaffy does not know the QC parameters for this array type. See the package vignette for details about how to specify QC parameters manually.
R gene chip mirna annotation package • 5.6k views
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Entering edit mode
Hii
I am working on the same problem.And I am beginer. If you already solved it, can you tell what has to been done.
Like what ypu mean by this. Already I have the cdf file.what has to done next ?? How can package installation be done.
##package installation from DOS shell (R CMD INSTALL "path to package")
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Entering edit mode

can you tell me where your miRNA-4_0-st-v1.cdf file come from. I am building a mirna41cdf annotation. but I am not this file. Finally,do you solve it? can you give me some advices? Thanks!

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Entering edit mode
6.9 years ago
Adamc ▴ 640

The only issue is with running the qc from simpleaffy- you can run some diagnostic plots yourself pretty easily, and everything else should run fine (normalization, limma, etc).

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