[BioC] RNA degradation problem

[fhong@salk.edu]

Hi Jim,
Thank you for your useful input.

> I find that the RNA degradation plots are less useful for indicating
> possible problems than the density plots.
Do you mean that "RNA degradation plots are less useful for indicating
 possible problems" or the problems indicated by RNA degradation plots are
less profound than those from density plots?


> If the density plots are all
> reasonably similar, in my experience the normalization should be fine.
> Another excellent plot for detecting problems is the residual plot in
> the affyPLM package.
Two questions here, thanks.
(1) Is it true that as long as the normalization is fine (for example, the
boxplot and density plot after normalization are similar among arrays), we
would proceed for further analysis.
(2) I did check the residual plot using affyPLM, P=please visit:
http://cactus.salk.edu/temp/QC_t.doc
What does it tell me? Some defects on the array?

Thank you very much for your kind help.

Many thanks!
Fangxin



>
> Best,
>
> Jim
>
>
>>
>> Many thanks!
>> Fangxin
>>
>>
>> --------------------
>> Fangxin Hong  Ph.D.
>> Plant Biology Laboratory
>> The Salk Institute
>> 10010 N. Torrey Pines Rd.
>> La Jolla, CA 92037
>> E-mail: fhong at salk.edu
>> (Phone): 858-453-4100 ext 1105
>>
>>
>>
>> --------------------
>> Fangxin Hong  Ph.D.
>> Plant Biology Laboratory
>> The Salk Institute
>> 10010 N. Torrey Pines Rd.
>> La Jolla, CA 92037
>> E-mail: fhong at salk.edu
>> (Phone): 858-453-4100 ext 1105
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
> --
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>
>


--------------------
Fangxin Hong  Ph.D.
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu
(Phone): 858-453-4100 ext 1105