[BioC] arrayQualityMetrics stringency & co

[Yannick Wurm]

Thanks for the quick and exhaustive reply!!

Regarding the missing heatmap - the files were indeed missing (this  
was on a g5 mac with 3 gigs of ram; R 2.7.2 with  
arrayQualityMetrics_1.6.1).
But when I reran arrayQualityMetrics on a linux machine with 64 gigs  
of ram the heatmap files were generated (this time under a freshly  
compiled R2.8 RC 2008-10-14 with arrayQualityMetrics_1.7.17).

Best,

Yannick

On Oct 16, 2008, at 12:08 , Audrey Kauffmann wrote:

> Hi Yannick,
>
> - 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.
> To decide whether or not you should remove some chips from your  
> analysis, I advice you to run the report after normalisation. If  
> after normalisation, some arrays are flagged with a star in several  
> quality assessment sections, I would remove it. Of course, it  
> mainly depends on the context. For instance, if there is a  
> biological good reason for an array to be an outlier, keep it.
>
> - To see the "inside" of the arrayQualityMetrics function:
> showMethods("arrayQualityMetrics")
> gives you the classes for which a method exists. Then you can see  
> the function for one of this class using selectMethod, for instance:
>
> selectMethod("arrayQualityMetrics","AffyBatch")
>
> However, if you are willing to modify it, you can download the  
> source of the package, the functions are in the directory  
> "arrayQualityMetrics/R".
> I am currently working on a new version of the package where it  
> will be easier to adapt the functions and to modify the report. If  
> you are interested, you can have a look at the devel branch of  
> Bioconductor, I will update the development version of the package  
> soon.
>
> - For the missing heatmap, I have sometimes seen that the plot is  
> done but for some reason does not show in the report. You can check  
> the files heatmap.png and heamapt.pdf in the directory where you  
> created the report.
>
> Audrey
>
>
> Yannick Wurm wrote:
>> Morning List,
>>
>> I've been toying with arrayQualityMetrics which gives me a great  
>> overview of my data without too much work.
>>
>> Several things are still unclear to me though:
>>
>>     - how does it calculate the '*' that indicate that a chip may  
>> be bad. How stringent/conservative are they? Because several of my  
>> spotted cDNA chips show up as having issues, and now I'm unsure  
>> whether or not I should remove them from my analysis.
>>
>>     - is there any way to "see inside" the package? I'd like to  
>> see how the stringency is calculated, and adapt some of the output  
>> formatting. But when I try to look inside, all I get is something  
>> called "environment":
>>         > arrayQualityMetrics
>>
>>         standardGeneric for "arrayQualityMetrics" defined from  
>> package "arrayQualityMetrics"
>>         function (expressionset, outdir = getwd(), force = FALSE,  
>> do.logtransform = FALSE,
>>             split.plots = FALSE, intgroup = "Covariate")
>>         standardGeneric("arrayQualityMetrics")
>>         <environment: 0x4882ad8>
>>         Methods may be defined for arguments: expressionset,  
>> outdir, force, do.logtransform, split.plots, intgroup
>>         Use  showMethods("arrayQualityMetrics")  for currently  
>> available ones.
>>         - on one NChannelSet containing 280 slides,  
>> arrayQualityMetrics didn't calculate the heatmap. But didn't  
>> display any error messages either. Possibly because of memory  
>> contraints on my 3GB mac?
>>
>> Thanks for putting me on the track to resolving this.
>>
>> Best,
>>
>> Yannick
>>
>> --------------------------------------------
>>          yannick . wurm @ unil . ch
>> Ant Genomics, Ecology & Evolution @ Lausanne
>>   http://www.unil.ch/dee/page28685_fr.html
>>
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>
> -- 
> Audrey Kauffmann
> EMBL - EBI
> Cambridge UK
> http://www.ebi.ac.uk/~audrey
>