[BioC] Detection Above Background (DABG) on Gene Level for Exon and Gene Arrays

[Pascal Gellert]

Dear Christian & Mark,

Thanks for your answer.

> HuGene arrays were originally designed by Affymetrix as arrays 
> measuring the transcript level and thus I assume they have tried to 
> select mainly probes which are not affected by alternative splicing, 
> so the statement may not apply. 
I am not sure, but at his point I think I have to disagree, because 
HuGene and HuExon have many (~65%) identical probes. This is from the 
Affymetrix Technical Note for HuGene:

"The Human Gene 1.0 ST Array design, wherever possible, uses a subset of 
the same probes on the Human Exon 1.0 ST Array to interrogate the more 
focused, better-annotated content at the gene level."

So this sounds like HuGene is designed from the core HuExon (but only 
two probes per probe set). It got additional probe sets for genes with 
few exons, but I am not sure if they avoided regions which are likely 
spliced?

> I guess to be really thorough, one could use the Affymetrix sample 
> data that's been run on 133+2, Gene ST and Exon ST platforms to see 
> how DABG compares to the old mas5calls on the same RNA
I think I really have to do this. It also would be interesting, if MAS5 
for HuGene and HuExon with the XPS package performs better than DABG.


Best regards,

Pascal


On 09/21/2010 11:18 PM, cstrato wrote:
> Dear Pascal,
>
> Dut to the design of xps it is not only able to support DABG calls at 
> both the probeset and transcript level, but does also support MAS5 
> detection calls for both Exon 1.0 ST and Gene 1.0 ST Arrays.
>
> To answer your question whether DABG is valid on the transcript level 
> I think you need to distinguish between HuExon and HuGene arrays:
>
> For HuExon arrays the statement of Affymetrix is probably true for 
> genes where alternative splicing occurs. However, HuGene arrays were 
> originally designed by Affymetrix as arrays measuring the transcript 
> level and thus I assume they have tried to select mainly probes which 
> are not affected by alternative splicing, so the statement may not apply.
>
> I would also be interested to hear from user experiences not only with 
> DABG on the transcript level but also with MAS5 calls on Exon ST and 
> Gene ST arrays. In my own experience the p-values between DABG and 
> MAS5 calls are almost identical for very low p-values but partly tend 
> to differ for larger p-values.
>
> Best regards
> Christian
> _._._._._._._._._._._._._._._._._._
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> _._._._._._._._._._._._._._._._._._
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>
> On 9/21/10 2:27 PM, Pascal Gellert wrote:
>> Hi all,
>>
>> The detection above background algorithm calculates a p-value for each
>> probe set, indication if this probe set is expressed or not (within the
>> background noise).
>> This is similar to the MAS5 detection calls, but Exon 1.0 ST and Gene
>> 1.0 ST Arrays don't have mismatch probes, therefore MAS5 cannot be used.
>>
>> According to Affymetrix, the DABG is not valid on gene level:
>>
>> "There is a strong assumption in DABG
>> that all the probes are measuring the same
>> thing (i.e., the same transcript). This is not
>> the case at the gene level due to alternative
>> splicing. For example, probes for a cassette
>> exon that is skipped will contribute to a mis-
>> leadingly insignificant p-value."
>>
>> To obtain, if a gene is expressed, often all probe sets of a gene were
>> used. If less than e.g. 50% of the exons of the gene are above a DABG
>> threshold, the gene is considered as not expressed.
>>
>> Nevertheless, the XPS package supports DABG on gene level. Does anyone
>> has experiences with DAGB on gene level?
>>
>> Thanks,
>>
>> Pascal Gellert
>>
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>