[BioC] OFF-TOPIC: Affy Scaling Factor and Absent/Present Calls
Laurent Gautier
laurent at cbs.dtu.dk
Fri Apr 18 06:57:09 MEST 2003
On Fri, Apr 18, 2003 at 11:36:39AM +0800, Adaikalavan Ramasamy wrote:
> Dear all,
>
> I have begun working with some affy data and there are some aspects of
> it that are confusing to me. The data was analysed using MAS 5.0 suite
> and most of the questions here pertain to single arrays (aka Absolute
> Analysis?).
Do you mean that you use the MAS software ? If this is the case,
we might be in the same position as you (i.e. with the official technical
documentation provided, especially the sadd_white-paper.pdf that
can be found on the website of the company). Did you read this document ?
Regards,
L.
>
> The first 3 question is on Scaling Factors (SF) which is defined as
>
> SF = TGT / x_96 ; where x_96 is the 2% trimmed mean
>
>
> 1. Why does MAS 5.0 apply the calculated SF to the middle 96% only and
> not 100% of the data ? Since it is often that SF > 1 and signal > 0 by
> affy's definition, the top 2% are being penalized. What is the rational
> behind this ?
>
> 2. I have read that a SF > 3 generally implies problems with the
> experiment. Why is this?
>
> 3. How is the target intensity, TGT, chosen ? Values of 100, 200, 500
> and even 1500 seem to have been chosen. Or do we choose TGT to ensure SF
> < 3 for most of the arrays.
>
>
> The next 2 are related to the Present/Absent calls provided.
>
> 4. I have 74 arrays and on average 50% of the data is missing. What is
> the normal/acceptable observed percentage missing.
>
> 5. I am removing all the signal data with Absent Call. Is this correct
> and is there any other use for Absent Call.
>
>
> Googling and reading the affy manuals (some parts of it anyway) has not
> cleared these confusions. Any answers, advices or references from this
> list is much appreciated. Thank you for your time.
>
> Regards, Adai.
>
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