[BioC] Quality Assessment

[Lana Schaffer]

Wolfgang,
You are correct in assuming that I am refering to the output of a recent 
devel-version of the affyQAReport function in the affyQCReport package.
R 2.5.0 Pre-release
library("affyQCReport")
library("affydata")
library(GeneMeta)
celpath <- "C:/.../"
CLL <- ReadAffy(celfile.path=celpath,widget=F)
rep2 = affyQAReport(CLL)
openQAReport(rep2)
Thank you for your helpful information.
Lana


----- Original Message ----- 
From: "Wolfgang Huber" <huber at ebi.ac.uk>
To: "Lana Schaffer" <schaffer at scripps.edu>
Cc: <bioconductor at stat.math.ethz.ch>
Sent: Thursday, January 18, 2007 11:59 AM
Subject: Re: [BioC] Quality Assessment


> Dear Lana,
> 
>> I am trying to understand the diagnostic plot of the MAD pairwise
>> differences of the M-values and how this plot can detect outliers.
>> I looked at the example for the CLL data and did not detect any
>> differences, but would like to know how to detect any differences.
>> All the small boxes are different colors but are mirrored pairwise 
>> intensities.   The notes say:  "Arrays whose distance matrix entries
>> are way different give cause for suspicion".  However, the color 
>> intensities look different??  Please explain how to know if they
>> are "way different".
> 
> Hmm, which package and function are you refering to and which version?
> 
> The following assumes that you refer to the output of a recent 
> devel-version of the affyQAReport function in the affyQCReport package?
> 
> The matrix is symmetric because the MAD distance is. More details are 
> given in the man page of "dist2". This is an exploratory plot that can 
> help detecting (a) outlier arrays and (b) batch effects. There are no 
> objective numeric thresholds when to call something an outlier, it 
> depends on your context, that's why the text is vague.
> 
> If there are outliers, you will expect to see vertical and horizontal 
> stripes in the plot of darker color. Batch effects that are aligned to 
> the order of the arrays as they are read in can be seen as blocks along 
> the diagonal. If you see neither, you are lucky, and the data passes 
> this quality criterion!
> 
> I have added some more text to explain this to the report template.
> 
> Hope this helps
>  Wolfgang
> 
> ------------------------------------------------------------------
> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
> 
> PS  Please do remember to state the output of sessionInfo() and the 
> relevant R code for reproducing the subject of your question.
> 
> 
>> 
>> Lana Schaffer
>> Biostatistics/Informatics
>> The Scripps Research Institute
>> DNA Array Core Facility
>> La Jolla, CA 92037
>> (858) 784-2263
>> (858) 784-2994
>> schaffer at scripps.edu
>> 
>