[BioC] .qcdef file

Leonor Palmeira palmeira at biomserv.univ-lyon1.fr
Thu Dec 17 17:45:56 CET 2009

Hello everybody,

this (old) thread was of very great help for my work on Bovine GeneChip. 
For the sake of archiving and for people out there working on unusual 
genomes, here is the bovinecdf.qcdef file I have built by looking for 
Gapdh and actin Probe Sets through the use of featureNames() on my chips:

array bovinecdf
alpha1 0.05
alpha2 0.065
spk bioB AFFX-r2-Ec-bioB-3_at
spk bioC AFFX-r2-Ec-bioC-3_at
spk bioD AFFX-r2-Ec-bioD-3_at
spk creX AFFX-r2-P1-cre-3_at
ratio actin3/actin5 AFFX-Bt-actin-3_at AFFX-Bt-actin-5_at
ratio actin3/actinM AFFX-Bt-actin-3_at AFFX-Bt-actin-M_at
ratio gapdh3/gapdh5 AFFX-Bt-gapd-3_at AFFX-Bt-gapd-5_at
ratio gapdh3/gapdhM AFFX-Bt-gapd-3_at AFFX-Bt-gapd-M_at



Hi Natassa,
  From that warning message, i'd change the first line to "array
drosophila2cdf" (without quotes).
If you perform RMA normalisation, get the probeset names that are on
the array via rownames(exprs(rmaData)), and make sure that the
probesetIDs that you've put in the qcdef file (AFFX-BioB-3_at etc...)
are actually on the chip.

I know the new generation "Gene/Exon ST" arrays now using numerical
probeset ID's, thus AFFX-BioB-3_at etc does not exist on these chips
any more.

On 26/06/2008, at 2:24 AM, ucbtagi at ucl.ac.uk wrote:

 > Hallo Mark,
 > Thanks for advise. I only changed the name array drosgenome1cdf to
 > array
 > drosgenome2cdf, saved it after adding an end of line in the R editor
 > (as
 > recommended by another user with problems!), then saved it in the
 > location
 > you recommended with the qcdef extension. After setting the
 > environment,
 > it still gives a warning :
 > (In qc.affy(unnormalised, ...) :CDF Environment name '
 > drosgenome2cdf '
 > does not match cdfname ' drosophila2cdf ')
 > but at least it now works.
 > I just hope I am not using the completely wrong correspondances, I
 > looked
 > at the Affymetrix website for more info on their array spike ins etc
 > but
 > it was not specific at all. I am waiting now for a reply from
 > Affymetrix
 > support. We could eventually have an official .qcdef file for
 > drosophila
 > users!
 > Kind regards,
 > Natassa
 >> hi Gioti,
 >> While I haven't made a qcdef file myself, I think I can still help;
 >> Second question first;
 >> This path is the correct location for the qcdef files. In my extdata
 >> folder (on Apple OSX this is /Library/Frameworks/R.framework/
 >> Versions/
 >> 2.6/Resources/library/simpleaffy/extdata) there are lots of other
 >> qcdef files in this directory which may help you make your own.
 >> First question, you will need to work out which ProbeSetID's on your
 >> chip correspond to the necessary ProbeSets for the qcdef file.
 >> Looking
 >> at various other qcdef files may help.
 >> For eg, all of the qcdef's that I have look VERY similar, and very
 >> much like this one (a drosophila genome 1 array)
 >> array drosgenome1cdf
 >> alpha1 0.04
 >> alpha2 0.06
 >> spk bioB AFFX-BioB-3_at
 >> spk bioC AFFX-BioC-3_at
 >> spk bioD AFFX-BioDn-3_at
 >> spk creX AFFX-CreX-3_at
 >> ratio actin3/actin5 AFFX-Dros-ACTIN_3_at AFFX-Dros-ACTIN_5_at
 >> ratio actin3/actinM AFFX-Dros-ACTIN_3_at AFFX-Dros-ACTIN_M_r_at
 >> ratio gapdh3/gapdh5 AFFX-Dros-GAPDH_3_at AFFX-Dros-GAPDH_5_at
 >> ratio gapdh3/gapdhM AFFX-Dros-GAPDH_3_at AFFX-Dros-GAPDH_M_at
 >> hope that helps,
 >> Mark
 >> On 25/06/2008, at 1:13 AM, ucbtagi at ucl.ac.uk wrote:
 >>> Dear all,
 >>> I am using AffyQCReport on my Drosophila  Genome2 genechip data, and
 >>> get
 >>> this error message:
 >>> Could not find array definition file ' drosophila2cdf.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.
 >>> Calls: qc -> qc -> qc.affy -> setQCEnvironment
 >>> Execution halted
 >>> I have downloaled the drosophila2cdf package and then, according to
 >>> the
 >>> vignette and the forum mails I ve seen so far, I should create a
 >>> drosophila2cdf.qcdef file myself. The thing is, i do not know how
 >>> parameters alpha, spike in etc should be set for the drosophila
 >>> array, it
 >>> is quite logic that the example text in the vignette can be
 >>> different as
 >>> it refers to the humam array... So fist question is, what exactly is
 >>> this
 >>> .qcdef file, and how do i write it for my arrays?
 >>> Second, where do i save it? Here is user's recommendations on the
 >>> forum, I
 >>> am wondering if those are applicable:
 >>> " Copy and paste the text below into bovinecdf.qcdef and save in
 >>> RHOME/library/simpleaffy/extdata. Eg.
 >>> /usr/local/lib/R/library/simpleaffy/extdata/bovinecdf.qcdef"
 >>> Thank you for help!
 >>> Gioti Anastasia
 >>> Institute of Healthy Ageing, and GEE
 >>> Room 326, The Darwin Building
 >>> University College London
 >>> Gower Street, London WC1E 6BT, UK.
 >>> _______________________________________________
 >>> Bioconductor mailing list
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