Question: miRNA microarray analysis
gravatar for aswathym
4.6 years ago by
United States
aswathym0 wrote:


I was working on this microRNA expression analysis. while doing I stuck by this error. Need to help to proceed further

Thank you

>data <- ReadAffy() 
AffyBatch object
size of arrays=541x541 features (18 kb)
cdf=miRNA-4_0 (??? affyids)
number of samples=4
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
In addition: Warning message:
missing cdf environment! in show(AffyBatch) 

I have searched to find solution for the cdf file.How to obtain a CDF 

microarray cdf • 1.9k views
ADD COMMENTlink modified 4.6 years ago by Gordon Smyth39k • written 4.6 years ago by aswathym0
Answer: miRNA microarray analysis
gravatar for James W. MacDonald
4.6 years ago by
United States
James W. MacDonald51k wrote:

You cannot use the affy/makecdfenv pipeline with these arrays. You should be using oligo instead.

dat <- read.celfiles(list.celfiles())
eset <- rma(dat)


ADD COMMENTlink written 4.6 years ago by James W. MacDonald51k

i did normalization. using the same procedure.

Thank you so much

ADD REPLYlink written 4.6 years ago by aswathym0
Answer: miRNA microarray analysis
gravatar for Johannes Rainer
4.6 years ago by
Johannes Rainer1.5k
Johannes Rainer1.5k wrote:

This basically means that the CDF package to work with this microarray is not available in Bioconductor. If you do have the CDF file yourself (usually you can find them at Affymetrix) you could try to create the package by yourself using the makecdfenv package, install it and then you should be able to process these arrays.

ADD COMMENTlink written 4.6 years ago by Johannes Rainer1.5k

Thank you sir

Still I tried all this. I couldn't understand what is the real problem.

 make.cdf.package("mirna40cdf", version = packageDescription("makecdfenv", field = "Version"), species="", unlink=TRUE, compress=FALSE, package.path = pkgpath)
Error in isCDFXDA(file.path(path.expand(cdf.path), filename)) : 

> make.cdf.package("mirna40.cdf", species = "mouse")
Error in isCDFXDA(file.path(path.expand(cdf.path), filename)) : 
  Unable to open the file D:/aswathy_works/hari_sir/KBH/mirna40.cdf

ADD REPLYlink written 4.6 years ago by aswathym0

do you have the mirna40.cdf file on your hand? if so, did you place it into the current directory? the last error message rather looks like the function is simply not finding your cdf file.

it actually looks that you can get the CDF from

ADD REPLYlink written 4.6 years ago by Johannes Rainer1.5k

sir I have the cdf file in the directory. Do I need to install in cmd ??

i have miRNA-4_0-st-v1 in my directory

I read somewhere like that.


ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by aswathym0

Sir I solved that problem

now its showing another

eset.rma <- expresso(abatch, bgcorrect.method="rma", normalize.method="quantiles", pmcorrect.method="pmonly", summary.method="medianpolish")
background correction: rma 
normalization: quantiles 
PM/MM correction : pmonly 
expression values: medianpolish 
background correcting...done.
Error in ans[[i]][, i.probes] : subscript out of bounds


why i just cant normalizing using




ADD REPLYlink written 4.6 years ago by aswathym0
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