Dear Bioconductor users, I used arrayQualityMetrics to generate quality report. But, in its summary report, how does it determine array which has potential problem or as being an outlier? I mean, is there some kind of cutoff for MA, Boxplot and heatmap? If it is yes, where can I find them? What is saturation effect? What is background intensity distributions. Dr. Hunber explained it before on how to interpret the *Standard deviation versus rank of the mean*, but I still do not understand its biological meaning. Thanks in advance. Yisong [[alternative HTML version deleted]]

Dear Yisong, I need to update the vignette to explain all of this. Here is how the outlier detection is performed: For the MA-plot, the mean of the absolute value of M is computed for each array and those that lie beyond the extremes of the boxplot's whiskers are considered as possible outliers arrays. The same approach, i.e. using the whiskers of the boxplot, is applied to the following: the mean and interquartile range (IQR) from the boxplots and NUSE, the sums of the rows of the distance matrix (for the heatmap), and the amplitude of low frequencies of the periodogram (for the spatial intensity distribution). In the case of the RLE plot, any array with a median RLE higher than 0.1 is considered as a possible outlier. I am not sure I understand what you mean by what is saturation effect and what is background intensity distributions. Do you want definition of what is saturation and background? Best regards, Audrey -- Audrey Kauffmann EMBL - EBI Cambridge UK http://www.ebi.ac.uk/~audrey > Dear Bioconductor users, > > I used arrayQualityMetrics to generate quality report. But, in its summary > report, how does it determine array which has potential problem or as being > an outlier? I mean, is there some kind of cutoff for MA, Boxplot and heatmap? If it is yes, where can I find them? > > What is saturation effect? What is background intensity distributions. Dr. > Hunber explained it before on how to interpret the *Standard deviation versus rank of the mean*, but I still do not understand its biological meaning. > > Thanks in advance. > > Yisong > > [[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 >