[BioC] Detection calls and LIMMA in GENE ST1.0

Mon Mar 7 21:32:58 CET 2011

Dear Jim, Sam, and Christian.

	I will look into all of your suggestions.
Expect more questions.

Best wishes,
Rich

On Mar 7, 2011, at 1:59 PM, James W. MacDonald wrote:

> Hi Rich,
>
> On 3/7/2011 1:30 PM, Richard Friedman wrote:
>> Jenny and list,
>>
>> Am I correct that P/M/A calls depend upon the presence of  
>> mismatched genes?
>> If so, is there a way to filter RMA normalized ST1.0 genes by present
>> absent?
>
> No, P/M/A are based on a Wilcoxon signed-rank test that compares the  
> expression levels of the PM and MM probes. If you don't have matched  
> PM and MM probes, you won't be able to do these calls.
>
> Best,
>
> Jim
>
>
>>
>> Thanks and best wishes,
>> Rich
>>
>>
>> On Mar 2, 2011, at 4:04 PM, Jenny Drnevich wrote:
>>
>>> Hi Rich,
>>>
>>> You can use the P/M/A calls to filter regardless of what
>>> pre-processing algorithm you use. It is a completely separate
>>> algorithm from MAS5, and I routinely use the P/M/A calls from the
>>> mas5calls() function in the affy package in conjunction with gcrma
>>> values.
>>>
>>> Cheers,
>>> Jenny
>>>
>>> At 01:14 PM 3/2/2011, Richard Friedman wrote:
>>>> Dear Gordon,
>>>>
>>>> Can you suggest how to define "some modest evidence of expression"
>>>> in Affymetrix arrays filtered with RMA
>>>> or GCRMA which does not give a presence-or-absence call?
>>>>
>>>> Thanks and best wishes,
>>>> Rich
>>>>
>>>> On Mar 1, 2011, at 7:50 PM, Gordon K Smyth wrote:
>>>>
>>>>> Deaer Avhena,
>>>>>
>>>>> I agree with Wolfgang that filtering is useful. In my lab, the
>>>>> standard practice is to filter probes that fail to show some  
>>>>> modest
>>>>> evidence for expression on at least n arrays, where n is the  
>>>>> minimum
>>>>> group size. For example, if we compare wt (with 2 replicate  
>>>>> arrays)
>>>>> to a mutant (with 3 replicate arrays), we filter probes that are
>>>>> Present on fewer than 2 arrays.
>>>>>
>>>>> This is because we want to keep any probe that is expressed in at
>>>>> least one of the experimental conditions. If a probe is expressed
>>>>> in one of the conditions, then it should appear consistently  
>>>>> across
>>>>> the replicates for that condition.
>>>>>
>>>>> Best wishes
>>>>> Gordon
>>>>>
>>>>>> Date: Mon, 28 Feb 2011 11:35:42 -0500
>>>>>> From: avehna <avhena at gmail.com>
>>>>>> To: whuber at embl.de
>>>>>> Cc: bioconductor at r-project.org
>>>>>> Subject: Re: [BioC] Detection calls and LIMMA
>>>>>>
>>>>>> Dear Wolfgang,
>>>>>>
>>>>>> Thank you for your response, I agree with you. I will read the
>>>>>> paper now...
>>>>>>
>>>>>> Best Regards,
>>>>>> Avhena
>>>>>>
>>>>>> On Mon, Feb 28, 2011 at 4:38 AM, Wolfgang Huber <whuber at embl.de>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi Avhena
>>>>>>>
>>>>>>> it is not required, but properly applied filtering can increase
>>>>>>> detection
>>>>>>> power in your experiment while still controlling type-I error  
>>>>>>> (false
>>>>>>> positives). The example you mention seems to be one that you  
>>>>>>> want
>>>>>>> to keep
>>>>>>> though, since it is a good candidate for being up-regulated in  
>>>>>>> the
>>>>>>> Treatment
>>>>>>> condition. One possibly reasonable criterion would be, e.g., to
>>>>>>> filter out
>>>>>>> all probesets that are called 'Absent' on all arrays. Some  
>>>>>>> further
>>>>>>> discussion on the topic is also here:
>>>>>>>
>>>>>>> [1] Bourgon, Gentleman and Huber. Independent filtering  
>>>>>>> increases
>>>>>>> detection
>>>>>>> power for high-throughput experiments. PNAS, 107(21):9546-9551,
>>>>>>>
>>>>>>> Best wishes
>>>>>>> Wolfgang
>>>>>>>
>>>>>>>
>>>>>>> Il Feb/28/11 6:51 AM, avehna ha scritto:
>>>>>>>
>>>>>>>> Hi All,
>>>>>>>>
>>>>>>>> I have a basic question. Is it required to filter the  
>>>>>>>> microarray
>>>>>>>> data
>>>>>>>> based
>>>>>>>> on the detection calls (A/M/P) before analyzing it with LIMMA?
>>>>>>>>
>>>>>>>> What if I have the following scenario (for example):
>>>>>>>>
>>>>>>>> Control Control Control Treatment
>>>>>>>> Treatment Treatment
>>>>>>>> 1367813_at A A P
>>>>>>>> P P P
>>>>>>>>
>>>>>>>> Please note that this gene is just "present/detected" once in  
>>>>>>>> the
>>>>>>>> Control,
>>>>>>>> but it is present in all the replicates of the treatment. In  
>>>>>>>> this
>>>>>>>> case:
>>>>>>>> what
>>>>>>>> would be the right thing to do? To eliminate it from the  
>>>>>>>> analysis
>>>>>>>> or keep
>>>>>>>> it
>>>>>>>> and consider it up or down depending on the signal of the
>>>>>>>> treatment?
>>>>>>>>
>>>>>>>> Thank a lot!
>>>>>>>> Avhena
>>>>>
>>>>> ______________________________________________________________________
>>>>> The information in this email is confidential and
>>>>> intend...{{dropped: 4}}
>>>>>
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>>>>
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>
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
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