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]]

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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >

Hi Louise, arrayQualityMetrics does not recognize weights on a RGlist. The best is to use the NA values. Best wishes, Audrey > 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]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > >