Yes, I fully concur.
 
G


________________________________

	From: James Anderson [mailto:janderson_net@yahoo.com] 
	Sent: 29 June 2007 20:04
	To: Hooiveld, Guido; bioconductor
	Subject: RE: [BioC] question about scale factor for Affy chip
	
	
	Yes, the calculation of absolute value of SF used 100 (500) as
reference, but in terms of the criterion: "SF should be within 3 fold of
each other", then 100 (500) does not play a role here. SF (10 15 20 25)
is the same as (30 45 60 75) in terms of the criterion, is that right?
	
	"Hooiveld, Guido" <Guido.Hooiveld@wur.nl> wrote: 

		Yep, but plz note that for the calculation of the SF no
reference array
		is used, but just a set value of 100 (500). This is in
contrast to e.g.
		dChip, in which of the [experimental] arrays is used as
reference, and
		therefore the set value varies between experiments.
		
		
		
		
		> -----Original Message-----
		> From: bioconductor-bounces@stat.math.ethz.ch 
		> [mailto:bioconductor-bounces@stat.math.ethz.ch] On
Behalf Of 
		> James Anderson
		> Sent: 29 June 2007 17:40
		> To: Hooiveld, Guido; bioconductor
		> Subject: Re: [BioC] question about scale factor for
Affy chip
		> 
		> Thanks for your email. So the criterion "SFs should be
within 
		> 3 fold" actually means that the ratio of the scale
factor of 
		> each array to the scale factor of the reference (mean)
array 
		> should be within 3 fold.
		> 
		> "Hooiveld, Guido" wrote: 
		> It is A, since you scale all arrays to the same target
value 
		> (100 is default in BioC, 500 is default in GCOS).
		> 
		> According to Affymetrix'criteria the difference
between the 
		> SFs should not vary more than a factor of 3. Since in
your 
		> case the SFs are within the same range (10.-10.2), the
SF 
		> does not indicate a problem. If you would have had
10.2. 
		> 10.1, 10.4, 40.9 and 2.7, the SF indiactes the last
two 
		> arrays deviate from the other arrays.
		> 
		> HTH,
		> Guido
		> 
		> 
		> > -----Original Message-----
		> > From: bioconductor-bounces@stat.math.ethz.ch
		> > [mailto:bioconductor-bounces@stat.math.ethz.ch] On
Behalf Of James 
		> > Anderson
		> > Sent: 29 June 2007 16:32
		> > To: bioconductor
		> > Subject: [BioC] question about scale factor for Affy
chip
		> > 
		> > Hi,
		> > 
		> > I am using the R package SimpleAffy, now I have a 
		> conceptual question 
		> > regarding the scale factor. Seems that Affymetrix
recommend 
		> the scale 
		> > factor should be within 3 fold, the way I understand
the 
		> scale factor 
		> > is that it is the ratio between the trimmed mean of
one chip 
		> > (normalized by MAS5) to the target value (say, 100
or 500). 
		> According 
		> > to the manual for QC in SimpleAffy:
		> > 
		> > "Large variations in scale factors signal cases
where the 
		> > normalisation assumptions are likely to fail due to
issues 
		> with sample 
		> > quality or amount of starting material."
		> > 
		> > I am getting a little confused about EXACTLY what
does scale factor 
		> > mean:
		> > A. The ratio between the trimmed mean of each chip
to a 
		> target value 
		> > B. The ratio between the trimmed mean of each chip
to the 
		> trimmed mean 
		> > of all the chips.
		> > 
		> > because the above section seems to me that as long
as there 
		> is small 
		> > variation in the scale factor, the quality is no
problem. 
		> What about 
		> > all the arrays have scale factor in the range
(10.1-10.2)? 
		> The scale 
		> > factor has almost no variation, but they are much
higher 
		> than 3. or I 
		> > am misunderstanding some part?
		> > 
		> > 
		> > Thanks a lot!
		> > 
		> > James
		> > 
		> > 
		> > ---------------------------------
		> > Pinpoint customers who are looking for what you
sell. 
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		> > 
		> > _______________________________________________
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		> >
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		> > 
		> 
		> 
		> 
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