Hi

I have certain data for clariom D

i need to generate CDF file also i want before normalisation and after normalisation plots

plots include:-

1)Box plot

2) density

3) MA plot

4) RNA degradation plot

5) NUSE plot

6) RLE plot

7) Heirahcial clustering plot

8) PCA plot

9) Corelation plot

No, you should not use / generate a CDF to analyze these arrays.

You rather should analyze these type of arrays using the package oligo (link) in combination with the corresponding platform design package (link). In the vignette (PDF) of oligo it is explained how to create the plots you are interested in (plots 1-6). For the other plots you can/should make use of other functions (e.g. hclust, prcomp [both from the default installed R package stats)].