problems using cdfenv
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Georg Otto ▴ 510
@georg-otto-956
Last seen 7.3 years ago
Dear bioconductors, i have a problem that presumably concerns my cdfenv installation. I use the zebrafish affymetrix gene chip, and I tried simpleaffy to get some quality control measures. Getting the expression measures with mas5 seems to work fine, but > qc<-qc(x, x.mas5) Gives me an error message: Error in qc.affy(unnormalised, ...) : I'm sorry I do not know about chip type: zebrafishcdf I installed the zebrafishcdf from the bioconductor website but i still get the same error. Then I made the cdf environment myself using the CDF file from Affymetrix and makecdfenv. Unfortunately there is still the same error. Is there something that I missed? Best regards, Georg
zebrafish cdf makecdfenv simpleaffy zebrafish cdf makecdfenv simpleaffy • 456 views
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@james-w-macdonald-5106
Last seen 11 hours ago
United States
Georg Otto wrote: > Dear bioconductors, > > i have a problem that presumably concerns my cdfenv installation. This not due to the cdfenv, but due to simpleaffy. Unfortunately simpleaffy is not set up to do qc on the zebrafish chips, which is what the error you get is indicating. For a list of chips that simpleaffy knows about, you can type '.nms' (without the quotes) at an R prompt after loading the simpleaffy package. Best, Jim > > I use the zebrafish affymetrix gene chip, and I tried simpleaffy to get > some quality control measures. Getting the expression measures with mas5 > seems to work fine, but > > > qc<-qc(x, x.mas5) > > Gives me an error message: > > Error in qc.affy(unnormalised, ...) : I'm sorry I do not know about chip > type: zebrafishcdf > > I installed the zebrafishcdf from the bioconductor website but i still > get the same error. Then I made the cdf environment myself using the CDF > file from Affymetrix and makecdfenv. Unfortunately there is still the > same error. > > Is there something that I missed? > > Best regards, > > Georg > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109
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