Question: problems using cdfenv
0
gravatar for Georg Otto
14.6 years ago by
Georg Otto510
Georg Otto510 wrote:
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
ADD COMMENTlink modified 14.6 years ago by James W. MacDonald50k • written 14.6 years ago by Georg Otto510
Answer: problems using cdfenv
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gravatar for James W. MacDonald
14.6 years ago by
United States
James W. MacDonald50k wrote:
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
ADD COMMENTlink written 14.6 years ago by James W. MacDonald50k
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