[BioC] RMA normalization

[Fangxin Hong]

when you perform normalization within tissue-of-origin, say only 2
replicated arrays for each tissue type, there is still a potential problem
that the normalized arrays are not comparable across different tissue
types. Like the intensities from arrays of one type tissue is
systematically higher tha that from arrays of another type tissue. This
sounds like a experimental issue, I am not a biologist. Anyone has idea
whether my concern is a problem or not in the real experiment.
Thanks

Fangxin

> I was under the impression getting a sufficient mRNA from a single
> sample was difficult enough.
>
> Sorry, I do not think I can be of much help as I never encountered this
> sort of problem, perhaps due to my own inability to distinguish the
> terms mRNA, sample, tissue. But there are many other people on the list
> who have better appreciation of biology and hopefully one of them could
> advise you.
>
> Could you give us the link to this message you are talking about.
>
>
>
> On Fri, 2004-09-10 at 15:26, Hairong Wei wrote:
>> Dear Adai:
>>
>> Thanks for asking.  I got this phrase from the messages stored in the
>> archive yesterday.  My understand is that, suppose you have 100 arrays,
>> and
>> 10 mRNA samples from 10 tissues.  Each 10 arrays are hybridized with
>> mRNAs
>> from the same tissue.  When you run RMA algoritm, you run those arrays
>> (10
>> each time) that hybridized with mRNA from same tissue together rathan
>> than
>> running 100 arrays together.  After running RMA for each tissue, the
>> scaling
>> is applied to arrays form different tissues.
>>
>> The reason for doing this is that it is not reasonable to assume that
>> the
>> arrays from different have the same distribution.
>>
>> What is you idea to do background.correction and normalization of 100
>> arrays
>> across 10 tissues?
>>
>> Thank you very much in advance
>>
>> Hairong Wei, Ph.D.
>> Department of Biostatisitics
>> University of Alabama at Birmingham
>> Phone:  205-975-7762
>>
>>
>>
>> -----Original Message-----
>> From: Adaikalavan Ramasamy [mailto:ramasamy at cancer.org.uk]
>> Sent: Thursday, September 09, 2004 5:09 PM
>> To: Hairong Wei
>> Cc: 'bioconductor at stat.math.ethz.ch'
>> Subject: Re: [BioC] RMA normalization
>>
>>
>> What do you mean by "normalization within tissue-of-origin" ? Can you
>> give us examples of these messages/papers/references discussing this.
>>
>> I often work with finding differentially expressed genes between two
>> phenotypes of the same type of cancer and tissue type. How would this
>> normalisation work then ?
>>
>> Regards, Adai
>>
>>
>>
>> On Thu, 2004-09-09 at 16:43, Hairong Wei wrote:
>> > I just started to work on low-level microarray data analysis and do
>> not
>> have
>> > experience in using RMA algorithm.   I am now in a situation where I
>> have
>> to
>> > normalize a a few hundred of arrays across multiple tissues.   I have
>> seen
>> a
>> > few messages regarding the legitimacy of using quantile-quantile (Q-Q)
>> > method to normalize many arrays across multiple tissue types in the
>> > bioconductor archive.   It seems that normalization within
>> tissue-of-origin
>> > was favored by some folks.  Although I feel it is the approach I
>> should
>> > take, I still hope to be more secure before I do it, just bacuse a lot
>> of
>> > work will be done on the normalized data.
>> >
>> > Can anybody help by pointing out a few references that use Q-Q method
>> within
>> > or not within tissue-of-origin?   For those who has done Q-Q within
>> the
>> > tissue-of-origin, could you please give some comments or your feelings
>> > regarding Q-Q withn tissue-of-origin?
>> >
>> > Hairong
>> >
>> > .
>> >
>> > _______________________________________________
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>> > Bioconductor at stat.math.ethz.ch
>> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>> >
>>
>
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-- 
Fangxin Hong, Ph.D.
Bioinformatics Specialist
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu