Question: GeneChip miRNA 4.0 processing in R - annotation data
0
gravatar for Jana
5.0 years ago by
Jana0
Jana0 wrote:

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.
ADD COMMENTlink modified 4.6 years ago by Adamc600 • written 5.0 years ago by Jana0
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")
ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by aswathym0

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!

ADD REPLYlink written 22 months ago by Forever0
0
gravatar for Adamc
4.6 years ago by
Adamc600
United States
Adamc600 wrote:

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).

ADD COMMENTlink written 4.6 years ago by Adamc600
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