[BioC] Error in setQCEnvironment(cdfn)

[James W. MacDonald]

Hi Suparna,

I use the oligo package to analyze these data, rather than the affy 
package. I also use my affycoretools package to help make certain QC 
plots that I like.

I tend to do something like

dat <- read.celfiles(list.celfiles(<wherever they are>))
hist(dat) ## gives a density plot - they should all look similar

You can look for problematic arrays using a probe level model. If you 
have multiple cores, you can first do
Sys.setenv(R_THREADS = <number of cores you want to use>)
plm <- fitProbeLevelModel(dat)

Then you can look at
NUSE(plm)
RLE(plm)

It may also be interesting to look at residuals
image(plm, type="residuals")

Then
eset <- rma(dat)

If you use affycoretools you can do

plotPCA(eset, <vector of numbers indicating group membership>, <group 
types>)

and see if your replicates are grouping together. You can also do MA plots

maplot(eset)

which compare all your chips to a pseudo-array. If  you have more than 
25 arrays, you should do 25 at a time.

Note that if you use the limma package to make comparisons you can 
weight arrays, so unless one or more are completely broken, you usually 
don't need to exclude. It's instructive to add the weights to a PCA 
plot. So if you have say 3 treated vs 3 control, you could do something like

trt <- factor(rep(c("Treated","Control"), each = 3))
design <- model.matrix(~trt)
wts <- arrayWeights(eset, design)

plotPCA(eset, groups, groupnames, addtext = round(wts, 2))

Best,

Jim

On 9/4/2012 12:06 PM, suparna mitra wrote:
> Dear Jim,
>   Thanks a lot. Yes I also read something that  HuGene array does not 
> use the T7-Oligo(dT) primer. But sorry being new I just missed the 
> point. Actually I was trying to follow a step by step tutorial for 
> Affy data.
>
> But can you suggest the best way to perform qc for this chip?
> Thanks a lot,
> Suparna.
>
> On 4 September 2012 16:58, James W. MacDonald <jmacdon at uw.edu 
> <mailto:jmacdon at uw.edu>> wrote:
>
>     Hi Suparna,
>
>
>     On 9/4/2012 11:35 AM, suparna mitra wrote:
>
>         Hello group,
>           I am new in bioconductor and trying use it for my Affymetrix
>         microarray
>         data.
>         Genechip HuGene-1_0-st-v1.
>
>
>     The simpleaffy package isn't really designed for this array. A
>     significant portion of the QC measures are based on comparisons
>     between the PM and MM probes, and the newer generation of arrays
>     from Affy no longer have MM probes.
>
>     Best,
>
>     Jim
>
>
>
>         I have normalized my data using rma. Then when I trying to see
>         the quality
>         I found following error. Can anybody help me with this please.
>         Thanks a lot in advance :)
>         Best wishes,
>         Suparna.
>
>             library(affy)
>             library(simpleaffy)
>
>         Loading required package: genefilter
>         Loading required package: gcrma
>
>         Attaching package: 'simpleaffy'
>
>         The following object(s) are masked _by_ '.GlobalEnv':
>
>              getBioC
>
>             library("hugene10stv1cdf")
>             aqc<-qc(InVivodata)
>
>         Error in setQCEnvironment(cdfn) :
>            Could not find array definition file ' hugene10stv1cdf.qcdef '.
>         Simpleaffy does not know the QC parameters for this array type.
>         See the package vignette for details about how to specify QC
>         parameters
>         manually.
>
>                 [[alternative HTML version deleted]]
>
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>
>     -- 
>     James W. MacDonald, M.S.
>     Biostatistician
>     University of Washington
>     Environmental and Occupational Health Sciences
>     4225 Roosevelt Way NE, # 100
>     Seattle WA 98105-6099
>
>
>
>
> -- 
> Dr. Suparna Mitra
> Wolfson Centre for Personalised Medicine
> Department of Molecular and Clinical Pharmacology
> Institute of Translational Medicine University of Liverpool
> Block A: Waterhouse Buildings,  L69 3GL Liverpool
>
> Tel.  +44 (0)151 795 5394, Internal ext: 55394
> M: +44 (0) 7511387895
> Email id: smitra at liverpool.ac.uk <mailto:smitra at liverpool.ac.uk>
> Alternative Email id: suparna.mitra.sm at gmail.com 
> <mailto:suparna.mitra.sm at gmail.com>
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099