[BioC] arrayQualityMetrics -weighted bad spots Imagene files

[audrey at ebi.ac.uk]

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
>
>
>
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