Question: Odd warning in simpleaffy, using quality control
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gravatar for Maciej Jończyk
7.2 years ago by
Maciej Jończyk720 wrote:
Hi David, > I'm trying to run some quality control (qc) on a bunch of raw files > retrieved from ArrayExpress, using simpleaffy, with the code: > > mixture.batch <- ReadAffy() > mixture.qc <- qc(mixture.batch) > > However, when I get to an experiment which has not used the > "hgu133plus2cdf" platform (In this case, it is experiment > E-GEOD-33443), I encounter a warning: > > > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain hugene10stv1.r3cdf > Library - package hugene10stv1.r3cdf not installed > Bioconductor - hugene10stv1.r3cdf not available > In addition: Warning message: > In qc.affy(unnormalised, ...) : > CDF Environment name ' hgu133plus2cdf ' does not match cdfname ' > hugene10stv1.r3cdf ' you need appropriate package containing cdf and probe info. see: http://www.bioconductor.org/packages/release/data/annotation/ there are hugene10stv1cdf and hugene10stv1probe, maybe it will fit your needs. Alternatively read about makecdf package. HTH -- Maciej Jonczyk, Department of Plant Molecular Ecophysiology Faculty of Biology, University of Warsaw 02-096 Warsaw, Miecznikowa 1 Poland -- This email was Anti Virus checked by Astaro Security Gateway. http://www.astaro.com
ADD COMMENTlink modified 7.2 years ago by David Westergaard280 • written 7.2 years ago by Maciej Jończyk720
Answer: Odd warning in simpleaffy, using quality control
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gravatar for David Westergaard
7.2 years ago by
David Westergaard280 wrote:
Hi Maciej, The cdf package is installed and working. (I've been preprocessing the same datafiles using 'affy') I still (almost) the same error: Attaching package: 'hugene10stv1cdf' The following object(s) are masked from 'package:hgu133plus2cdf': i2xy, xy2i Error: NAs in foreign function call (arg 1) In addition: Warning message: In qc.affy(unnormalised, ...) : CDF Environment name ' hgu133plus2cdf ' does not match cdfname ' hugene10stv1cdf ' I might have missunderstood something. Does the qc function in simpleaffy not recognize cdfName by itself, or do I have to specify it? Best, David 2012/2/27 Maciej Jo?czyk <mjonczyk at="" biol.uw.edu.pl="">: > Hi David, > > >> I'm trying to run some quality control (qc) on a bunch of raw files >> retrieved from ArrayExpress, using simpleaffy, with the code: >> >> mixture.batch <- ReadAffy() >> mixture.qc <- qc(mixture.batch) >> >> However, when I get to an experiment which has not used the >> "hgu133plus2cdf" platform (In this case, it is experiment >> E-GEOD-33443), I encounter a warning: >> >> >> Error in getCdfInfo(object) : >> ?Could not obtain CDF environment, problems encountered: >> Specified environment does not contain hugene10stv1.r3cdf >> Library - package hugene10stv1.r3cdf not installed >> Bioconductor - hugene10stv1.r3cdf not available >> In addition: Warning message: >> In qc.affy(unnormalised, ...) : >> ?CDF Environment name ' hgu133plus2cdf ' does not match cdfname ' >> hugene10stv1.r3cdf ' > > > you need appropriate package containing cdf and probe info. > > see: > http://www.bioconductor.org/packages/release/data/annotation/ > > there are hugene10stv1cdf and hugene10stv1probe, maybe it will fit your > needs. > Alternatively read about makecdf package. > > HTH > > -- > Maciej Jonczyk, > Department of Plant Molecular Ecophysiology > Faculty of Biology, University of Warsaw > 02-096 Warsaw, Miecznikowa 1 > Poland > > > > -- > This email was Anti Virus checked by Astaro Security Gateway. > http://www.astaro.com
ADD COMMENTlink written 7.2 years ago by David Westergaard280
> The cdf package is installed and working. (I've been preprocessing > the > same datafiles using 'affy') I still (almost) the same error: > > Attaching package: 'hugene10stv1cdf' > > The following object(s) are masked from 'package:hgu133plus2cdf': > > i2xy, xy2i > > Error: NAs in foreign function call (arg 1) > In addition: Warning message: > In qc.affy(unnormalised, ...) : > CDF Environment name ' hgu133plus2cdf ' does not match cdfname ' > hugene10stv1cdf ' > > I might have missunderstood something. Does the qc function in > simpleaffy not recognize cdfName by itself, or do I have to specify > it? Hi David, For me it seems that in R environment you have loaded hgu133plus2cdf and it persists after installation of hugene10stv1cdf package. From simple.affy package: " qc.affy(unnormalised,normalised=NULL,tau=0.015,logged=TRUE, cdfn=cdfName(unnormalised)) " cdfn option: "The cdf name for the array - can be used to specify a different set of probes to the default" Maybe try to specify correct cdf using cdfn option. HTH, Maciej
ADD REPLYlink written 7.2 years ago by Maciej Jończyk720
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