[BioC] quality control and normalisation; RNA degradation problem

[Margaret Gardiner-Garden]

Dear Fangxin, 

My feeling is that StemT2 has such a different distribution to the other
chips that it should not be included in the analysis.  

It is a tricky question though because the shape of the density distribution
of StemT2 looks more like the shape we expect in a good quality chip, but
StemT2 has a very low intensity for an affy chip (compared to our chips).
How much sample RNA are you using for each chip...could you have used less
for StemT2 or could the hybridization have been not as good for StemT2?

I was wondering if the Bioconductor community knew if there is any
evidence/guide for how different a distribution has to be before the chips
should not be normalized together?  This is a question we come up against
again and again (especially when analyzing published data sets). 

Regards
Marg

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of fhong at salk.edu
Sent: Thursday, 19 January 2006 4:45 AM
To: James W. MacDonald
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] RNA degradation problem

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

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