Hi
I have 40 samples for human clariom D chip.
I need CDF file in environment for running any analysis using affy package.
So how to make custom cdf file for clariom D human chip in R
As i can see it is not available in affymetrix website.
Mmm, did I not basically answer your question in this thread? A: how to generate CDF and before normalisation and after normlisation plot for Cla
Also, if you did some searching on (for example) this forum you would have learned that for the newest generation of Affymetrix arrays CDF files are not anymore provided (and used). see e.g. cdf file for Clariom S Human HT. The packages oligo or xps are the way to go to analyze these arrays!
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version 2.3.6
Agree but i need to do RMA-Alt-splicing Normalisation so for this i need to have CDF file
What exactly is "RMA-Alt-splicing Normalisation"? Has it to do with the (non-Bioconductor) software 'AltAnalyze'? In any case, I am not familiar with both, but a quick glance at 'AltAnalyze' suggested to me that it makes use of Affymetrix Power Tools (APT), which uses the files than can be downloaded directly from Affymetrix (Thermo). Please realize that Affymetrix (also) does not provide CDFs for these newest arrays!
So i can not use package like affy etc . Because if i use also it ask CDF into enviorment .