Question: How to make custom CDF file for Clariom D human chip
0
gravatar for kritikamish99
19 months ago by
India
kritikamish9910 wrote:

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.

 

 

cdf clariom d • 369 views
ADD COMMENTlink modified 19 months ago by Guido Hooiveld2.5k • written 19 months ago by kritikamish9910
Answer: How to make custom CDF file for Clariom D human chip
0
gravatar for Guido Hooiveld
19 months ago by
Guido Hooiveld2.5k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.5k wrote:

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!
 

ADD COMMENTlink modified 19 months ago • written 19 months ago by Guido Hooiveld2.5k

Agree but i need to do RMA-Alt-splicing Normalisation so for this i need to have CDF file

ADD REPLYlink written 19 months ago by kritikamish9910

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!

ADD REPLYlink written 19 months ago by Guido Hooiveld2.5k

So i can not use package like affy etc . Because if i use also it ask CDF into enviorment .

ADD REPLYlink written 19 months ago by kritikamish9910
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