[BioC] Analyzing mulitple tissues

Gordon Smyth smyth at wehi.edu.au
Wed Jun 8 10:28:53 CEST 2005

The importance of using RMA or GCRMA rather than MAS is far greater than 
the impact of the factors you're discussing here. Furthermore, quantile 
normalisation is not designed to be used in conjunction with MAS and 
probe-set filtering.

RMA will work best on all the chips at once, so I would personally do that. 
Simplest and best.


At 04:52 PM 8/06/2005, Uri David Akavia wrote:
>Gordon Smyth wrote:
>>There isn't any conflict between Naomi's comments and my own. Naomi 
>>actually refered to "biological replication" rather than to replication 
>>per se. She was reacting to Uri's original post which made it very 
>>unclear whether there is any biological replication in his experiment at 
>>all, i.e., it may be that Cardiac1, Cardiac2 etc are not in fact 
>>biological replicates. Replication is a subtle business, and Uri would 
>>need to describe his process and population in much more detail than he 
>>done for more to be said. I may be wrong, but I doubt that Naomi was 
>>especially concerned about the single MSC chip.
>Actually, you're correct.
>Cardiac1, Cardiac2 are different stages of the same tissue.
>They are NOT biological replicates.
>However, I think my question was misunderstood.
>I use quantile normalization and select genes by fold change.
>I wish to see the differentiation of Cardiac, and to compare Cardiac to MSC.
>My question is: Should I normalize on all tissues, or simply on the 
>tissues analyzed at the time?
>If I normalize all 6 samples, I'm afraid that the smaller differences 
>between Cardiac will be masked by the larger differences between Cardiac 
>and MSC.
>If I normalize only the tissues analyzed, it means that I will normalize 
>multiple times, each time differently for different tissue (leading to 
>different values).
>What is preferable? What are additional pros and cons for each method?
>Thank you,
>Uri David Akavia

More information about the Bioconductor mailing list