[BioC] technical replicates

William Kenworthy W.Kenworthy at murdoch.edu.au
Tue Jan 13 03:15:51 MET 2004

Unfortunately, they came to us too late and were forced by circumstances
to complete the experiment as designed.  Next time ...

I am thinking a straight average of the replicate values for each gene
may the best solution (not per probe).  However, a significance value
may show up a suspect gene (if a difference exists across the
replicates, something is wrong in a yes/no fashion, rather than looking
at degrees of significance)

My preference is to use RMA from the affy package as a first pass, then
expand using some of the other algorithms but concrete examples (and
documentation) on how to specify replicates is lacking.  (i.e., the data
examples say there are replicates, but how are they specified/handled -
or not?)


On Sun, 2004-01-11 at 23:03, Naomi Altman wrote:
> I usually use mixed model ANOVA to determine differential expression.  By 
> putting in a random effects term for sample (you have 2 technical reps per 
> sample) you end up with the correct analysis.
> However, in your case you have no sample replication.  As a result, you 
> cannot do a statistically valid ANOVA.   People do use various 
> approximations - the Affy-type Wilcoxon tests which treat the probes as 
> replicates (makes me very very nervous); using the technical replicates as 
> if they were biological replicates (makes me very nervous - there is no 
> guarantee that there is much relationship between the technical and 
> biological variation).  Of course, the best thing to do is to convince the 
> investigators that biological replication is far more important than 
> technical replication.  In most Affy studies, technical replication will 
> not be cost-effective due to the relatively small technical variance and 
> the large cost of individual arrays.
> At 01:18 AM 1/9/2004, William Kenworthy wrote:
> >Hi, I have just been passed a set of affy data that consists of 3
> >states, two technical replicates of each state (6 chips overall)
> >
> >1. whats the best way (normalisations, algorithms) to leverage technical
> >replicates?
> >
> >2. how do you tell algorithms such as rma which are the replicates?  (I
> >presume the phenoData in the AffyBatch specifies this, but the examples
> >are in a binary format so you cant open the raw data file and see how
> >they are put together!)
> >
> >BillK
> >
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> Naomi S. Altman                                814-865-3791 (voice)
> Associate Professor
> Bioinformatics Consulting Center
> Dept. of Statistics                              814-863-7114 (fax)
> Penn State University                         814-865-1348 (Statistics)
> University Park, PA 16802-2111

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