RLE AND NUSE plots

Affy QC plots for exon arrays ...

One method of deciding whether or not an array is problematics from a quality standpoint is NUSE. The goal of NUSE is to identify any arrays which have elevated standard errors relative to other arrays in the dataset. This is done by standardizing the SE across arrays to have median 1 for each probeset. Our graphical tool consists of boxplots of these quantities for each array. A discordant boxplot indicates it is of poorer quality relative to the rest of the dataset. Instead of visually examining these quantities suitable numerical summaries such as the median and IQR NUSE could be used.

Another tool for making a decision about whether an array should be removed from subsequent analysis because of poor quality is RLE. These are the log-scale expression values relative to the median expression value computed on a probeset by probeset basis. a significantly different boxplot indicates problem.

aroma.affymetrix and other lots of packages allows to plot RLE and NUSE.

The NUSE is generally considered more sensitive than the RLE.

Bioconductor post on using arrayQualityMatrics with exon arrays

Looks like both simpleaffy and arrayQualityMetrics have problem with QCing Affy Exon 1.0 ST arrays.

Though following post does suggest a way to put custom CDF.


Hi Gard,

Sorry for the delay answering. I do not have much experience using
arrayQualityMetrics for Exon arrays, so I have talked with Crispin Miller
(simpleaffy package) about it and according to him "most of the Affymetrix
QC metrics for the 3' IVT arrays aren't directly applicable to the exon
arrays. They rely on MAS 5 and paired MM spots (neither of which are
applicable for exon arrays) and also make assumptions on 3'/5' ratios that
don't apply because the exon array chemistry is different."
I have now modified the package and version 2.4.3 of arrayQualityMetrics
should not perform the QC statistics from simpleaffy when "exon" is in the
cdfname.

Best wishes,
Audrey

> Hi.
>
> I am trying to get the arrayQualityMetrics package to run on a set of
CEL files from the Human Exon array from Affymetrix
>
> My problems begin when I want to run the arrayQualityMetrics function
and it gives the following error message :
>
> running R 2.9.2 and bioconductor version 2.4
>
> >library(affy)
> >library(simpleaffy)
> >ibrary(arrayQualityMetrics)
> >ecesbatch<-read.affybatch("H1.CEL", "H2.CEL", "H3.CEL", "H4.CEL",
> "H5.CEL", "H6.CEL", "H7.CEL", "H8.CEL", "H9.CEL", "H10.CEL",
> "H11.CEL", "H12.CEL", "H13.CEL", "H14.CEL", "H15.CEL", "H16.CEL")
>
> ## attach cdf to expr set
> ecesbatch cdfName <- "exon.pmcdf" ## this is a cdf file from the XMAP
website
>
> #Check the name is correct for the cdf file (unneccessary)
> > cdfname <- cleancdfname(cdfName(ecesbatch))
> > cdfname
> [1] "exon.pmcdf"
>
> >arrayQualityMetrics(expressionset = ecesbatch,outdir =
> "output",force = TRUE,do.logtransform = TRUE)
>
> This cmd runs for a very long time and generates a bunch of .pdfs and
.pngs and an empty QCReport.html file.
> And R says there is an error sonce the arrayQualityMetrics package does
not know the QCparameters of this chip.
>
>
> I have found an instruction from C. Miller (one of the persons behind
simpleaffy) about how use the three functions provided by the
> simpleaffy package, or to make the needed .qcdf file:
> I need alpha values (that is okay) and I need control and spike
> probeIDs.
>
> I am using the Human Exon array 1.0 from affymetrix, and I do not know
what to fill in in the .qcdf file,
> anyone who knows how to get by this problem?
> Trying to get the probenames to set the values I ran into another problem..
>
> > prbs <- ls(cdfname)
> Error in as.environment(pos) :
> no item called "exon.pmcdf" on the search list
> >
>
> crashes like this shown here.
>
>
> Please if anyone knows or has an idea, basicly what I need is
> the .qcdf file for the HUman Exon array from Affy.
> Best regards
> Gard
>
> #################################
> Gard Thomassen
> Ph.D student CMBN, Rikshospitalet, Oslo
> Bioinformatician, Radiumhospitalet, Oslo
> Norway
> Email : gardt@...
> Office: + 47 22781736
> Phone +47 93674926