[BioC] some mismatches between affymetrix CGOS MAS5 detection calls and BioC mas5calls

[Kasper Daniel Hansen]

If you read the man page for the mas5calls you will also see that the  
BioC implementation is only approximately equal to the calls made by  
the MAS5 software. So you should expect some differences.

Kasper

On Dec 11, 2006, at 6:26 AM, Morten Mattingsdal wrote:

> hello haiyan,
> The "M" is a marginal call, and is a borderline "P" or "A". I think  
> its
> common to consider a "marginal call" a "present call".
> morten
>
> haiyan wu wrote:
>> Hi,all
>> Recently I download some CEL files from GEO and get it's detection
>> calls using BioC mas5calls . When I compare this file with  
>> standard file
>> produced by Affymetrix company's CGOS platform,I found there are  
>> about 300
>> probesets called "M" by mas5call function but called "P" in my  
>> standard
>> file. These mismatches may affect our analysis result if we use  
>> detection
>> calls as a filter condition or for special algorithm using calls
>> infomation.  For many of us ,one may download CEL files from GEO or
>> ArrayExpress but can not get raw files contain detection calls  
>> from those
>> website.So we use BioC's mas5call function.But there are  
>> differences between
>> two method! What should I do?
>>
>> Regards
>>
>> haiyan
>>
>> 	[[alternative HTML version deleted]]
>>
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