SimpeAffy: how to get/generate qcdef file?
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@renaud-gaujoux-3125
Last seen 7.1 years ago
Great thanks. All right, I tried it but I got these error messages: Again unable to find the file even if I ran a setQCEnvironment giving the clean name and the path to the file. > AffyQA(parameters = c("part"), raw = eset) [1] "Retrieving grouping parameters" Error in setQCEnvironment(genome) : Could not find array definition file ' sugarcanecdf.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. or if running qc from simpleaffy directly: > qc(eset) Error in FUN(c("AFFX-Sof-actin-3_a_at", "AFFX-Sof-actin-5_a_at", "AFFX-Sof-actin-M_a_at", : subscript out of bounds I've checked that the probe "AFFX-Sof-actin-3_a_at" exist on the array via: > x.mas5 <- call.exprs(eset,"mas5") > idx = which(rownames(exprs(x.mas5)) == "AFFX-Sof-actin-3_a_at") > idx [1] 57 > exprs(x.mas5)[idx,] Any ideas? Thanks, Renaud claire wilson wrote: > yes > > 2009/2/5 Renaud Gaujoux <renaud at="" cbio.uct.ac.za=""> <mailto:renaud at="" cbio.uct.ac.za="">> > > Do you mean this definitions are for the sugar cane array? > > claire wilson wrote: > > Take a look at NetAffx/the probe control sequences file on the > Affy website to find out what the probesets are for the > control genes or look in the .psi file (I got the probesets > below from here). alpha1 and alpha2 can stay as they are (as > indicated in the .cif file), this should get you started > > claire > > array <insert cdf="" name="" here=""> > 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-Sof-actin-3_a_at AFFX-Sof-actin- 5_a_at > ratio actin3/actinM AFFX-Sof-actin-3_a_at AFFX-Sof-actin- M_a_at > ratio gapdh3/gapdh5 AFFX-Sof-gapdh-3_at AFFX-Sof-gapdh-5_at > ratio gapdh3/gapdhM AFFX-Sof-gapdh-3_at AFFX-Sof-gapdh-M_at > > from the cif file > ;P/A Call Parameters > ;P/A: Thresholds > MinAlpha1=0 > MinAlpha2=0 > Alpha1=0.050000 > Alpha2=0.065000 > DefAlpha1=0.050000 > DefAlpha2=0.065000 > MaxAlpha1=0.5 > MaxAlpha2=0.5 > > 2009/2/5 Renaud Gaujoux <renaud at="" cbio.uct.ac.za=""> <mailto:renaud at="" cbio.uct.ac.za=""> <mailto:renaud at="" cbio.uct.ac.za=""> <mailto:renaud at="" cbio.uct.ac.za="">>> > > > Hi, > > I actually read the vignette but how do you get all the > information needed to create the file? I guess the qcdef file > showed in vignette will not work as it is for a sugar cane > array > (even changing the header name to sugarcanecdf). > > Do I have to look by eye at the cdf file and extract the > info? In > that case how do I know which control probe to chose? all > of them? > It seems to me that the kind of information required can be > found > automatically. I am not familiar with the Affy cdf format so I > find it a bit tricky to do that by hand. > Is there some procedure to follow to find the correct > information > in the file? > > Thanks. > Renaud > > > claire wilson wrote: > > Hi Renaud > > see page 13 of the vignette for details on how to create a > qcdef file > > > http://bioconductor.org/packages/2.3/bioc/vignettes/simplea ffy/inst/doc/simpleAffy.pdf > > hth > > claire > > > > > > -- > http://claire.wilson.googlepages.com/ > > > > > > -- > http://claire.wilson.googlepages.com/ >
cdf probe affy simpleaffy cdf probe affy simpleaffy • 1.1k views
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@claire-wilson-3267
Last seen 7.1 years ago
I had some problems with that too and found it worked when i did this # change directory to current location of qcdef file qcdef.location = getwd() setQCEnvironment("customArraycdf",qcdef.location ) if that doesnt help, I am stumped! perhaps crispin miller can help as he is the package author claire 2009/2/5 Renaud Gaujoux <renaud@cbio.uct.ac.za> > Great thanks. > > All right, I tried it but I got these error messages: > > Again unable to find the file even if I ran a setQCEnvironment giving the > clean name and the path to the file. > > AffyQA(parameters = c("part"), raw = eset) > [1] "Retrieving grouping parameters" > Error in setQCEnvironment(genome) : > Could not find array definition file ' sugarcanecdf.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. > > or if running qc from simpleaffy directly: > > > qc(eset) > Error in FUN(c("AFFX-Sof-actin-3_a_at", "AFFX-Sof-actin-5_a_at", > "AFFX-Sof-actin-M_a_at", : > subscript out of bounds > > I've checked that the probe "AFFX-Sof-actin-3_a_at" exist on the array via: > > > x.mas5 <- call.exprs(eset,"mas5") > > idx = which(rownames(exprs(x.mas5)) == "AFFX-Sof-actin-3_a_at") > > idx > [1] 57 > > exprs(x.mas5)[idx,] > > Any ideas? > > Thanks, > Renaud > > claire wilson wrote: > >> yes >> >> 2009/2/5 Renaud Gaujoux <renaud@cbio.uct.ac.za <mailto:="">> renaud@cbio.uct.ac.za>> >> >> Do you mean this definitions are for the sugar cane array? >> >> claire wilson wrote: >> >> Take a look at NetAffx/the probe control sequences file on the >> Affy website to find out what the probesets are for the >> control genes or look in the .psi file (I got the probesets >> below from here). alpha1 and alpha2 can stay as they are (as >> indicated in the .cif file), this should get you started >> >> claire >> >> array <insert cdf="" name="" here=""> >> 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-Sof-actin-3_a_at AFFX-Sof-actin- 5_a_at >> ratio actin3/actinM AFFX-Sof-actin-3_a_at AFFX-Sof-actin- M_a_at >> ratio gapdh3/gapdh5 AFFX-Sof-gapdh-3_at AFFX-Sof-gapdh-5_at >> ratio gapdh3/gapdhM AFFX-Sof-gapdh-3_at AFFX-Sof-gapdh-M_at >> >> from the cif file >> ;P/A Call Parameters >> ;P/A: Thresholds >> MinAlpha1=0 >> MinAlpha2=0 >> Alpha1=0.050000 >> Alpha2=0.065000 >> DefAlpha1=0.050000 >> DefAlpha2=0.065000 >> MaxAlpha1=0.5 >> MaxAlpha2=0.5 >> >> 2009/2/5 Renaud Gaujoux <renaud@cbio.uct.ac.za>> <mailto:renaud@cbio.uct.ac.za> <mailto:renaud@cbio.uct.ac.za>> >> <mailto:renaud@cbio.uct.ac.za>>> >> >> >> Hi, >> >> I actually read the vignette but how do you get all the >> information needed to create the file? I guess the qcdef file >> showed in vignette will not work as it is for a sugar cane >> array >> (even changing the header name to sugarcanecdf). >> >> Do I have to look by eye at the cdf file and extract the >> info? In >> that case how do I know which control probe to chose? all >> of them? >> It seems to me that the kind of information required can be >> found >> automatically. I am not familiar with the Affy cdf format so I >> find it a bit tricky to do that by hand. >> Is there some procedure to follow to find the correct >> information >> in the file? >> >> Thanks. >> Renaud >> >> >> claire wilson wrote: >> >> Hi Renaud >> >> see page 13 of the vignette for details on how to create a >> qcdef file >> >> >> http://bioconductor.org/packages/2.3/bioc/vignettes/simpleaffy/inst /doc/simpleAffy.pdf >> >> hth >> >> claire >> >> >> >> >> >> -- http://claire.wilson.googlepages.com/ >> >> >> >> >> >> -- >> http://claire.wilson.googlepages.com/ >> >> > -- http://claire.wilson.googlepages.com/ [[alternative HTML version deleted]]
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