[BioC] question about scale factor for Affy chip
Guido.Hooiveld at wur.nl
Fri Jun 29 19:58:18 CEST 2007
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 at stat.math.ethz.ch
> [mailto:bioconductor-bounces at 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" <Guido.Hooiveld at wur.nl> 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.
> > -----Original Message-----
> > From: bioconductor-bounces at stat.math.ethz.ch
> > [mailto:bioconductor-bounces at 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).
> > 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
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