Question: how to generate CDF and before normalisation and after normlisation plot for Clariom D
0
gravatar for kritikamish99
19 months ago by
India
kritikamish9910 wrote:

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

 

clariom d • 253 views
ADD COMMENTlink modified 19 months ago by Guido Hooiveld2.5k • written 19 months ago by kritikamish9910
Answer: how to generate CDF and before normalisation and after normlisation plot for Cla
0
gravatar for Guido Hooiveld
19 months ago by
Guido Hooiveld2.5k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.5k wrote:

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)].

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