[BioC] Detection calls and LIMMA

Jenny Drnevich drnevich at illinois.edu
Wed Mar 2 22:04:28 CET 2011

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.


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,
>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
>>>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,
>>>On Mon, Feb 28, 2011 at 4:38 AM, Wolfgang Huber <whuber at embl.de>
>>>>Hi Avhena
>>>>it is not required, but properly applied filtering can increase
>>>>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
>>>>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
>>>>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
>>>>>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
>>>>>but it is present in all the replicates of the treatment. In this
>>>>>would be the right thing to do? To eliminate it from the analysis
>>>>>or keep
>>>>>and consider it up or down depending on the signal of the
>>>>>Thank a lot!
>>The information in this email is confidential and intend...{{dropped: 4}}
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