[BioC] arrayQualityMetrics -weighted bad spots Imagene files

audrey at ebi.ac.uk audrey at ebi.ac.uk
Fri Mar 27 18:06:12 CET 2009

Hi Louise,

arrayQualityMetrics does not recognize weights on a RGlist. The best is to
use the NA values.

Best wishes,

> Hi Audrey
> Thanks very much for replying. Yes it does help!
> Does the arrayqualitymetrics call recognize weights on a the RGList
> or is it best to set for example a flagged R and G intensity value as NA
> or should we try and remove that spot completely?
> (Hope that makes sense?)
> ________________________________
> From: "audrey at ebi.ac.uk" <audrey at ebi.ac.uk>
> To: Louise Donnison <louiseusergroup at yahoo.co.uk>
> Cc: bioconductor at stat.math.ethz.ch
> Sent: Friday, 27 March, 2009 2:09:35
> Subject: Re: [BioC] arrayQualityMetrics -weighted bad spots Imagene files
> Hi Louise,
> On the spatial distribution plot given by arrayQualityMetrics, you should
> have black squares for missing values as well. For the other plots, the
> missing values are disregarded.
> arrayQualityMetrics does not treat specially the missing values in the
> evaluation of the outlier arrays. I mean, if an array has more missing
> values than the others, it will not be weighted or anything. But, it will
> naturally contributes to its difference with the other arrays.
> Hope that helps,
> Audrey
>> Hi
>> How does arrayQualityMetrics handle spots that have been flagged as bad,
>> those values that are thus missing? We are using imagene files and we
>> can
>> generate
>> maQualityPlots and set a badspotfunction parameter to identify bad
>> spots.
>> This allows us to see on a spatial plot flaged spots as black sqaures.
>> Do you have any suggestions as what we can do with these flagged values
>> for use in arrayQualityMetrics? How does arrayQualityMetrics handle
>> missing values?
>> regards
>> Louise
>>     [[alternative HTML version deleted]]
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