Question: Odd warning in simpleaffy, using quality control
0
7.2 years ago by
ejulia10
ejulia10 wrote:
Maciej Jo?czyk <mjonczyk at="" ...=""> writes: > > > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at ... > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > Dear all, in particularly Maciej and David, I'm wondering if you could help me. I've been having about the kind of problems as David's initial email mentioned. Following Maciej's advice I installed cdf environments and tried to specify them when calling qc.affy(), but I'm still stuck - see below for the relevant commands from my R consule. > D.Affy.qc<-qc.affy(D) Error in FUN(c("AFFX-HSAC07/X00351_3_at", "AFFX-HSAC07/X00351_5_at", "AFFX-HSAC07/X00351_M_at", : subscript out of bounds In addition: Warning message: In qc.affy(D) : CDF Environment name ' hgu95av2cdf ' does not match cdfname ' drosgenome1cdf ' > D.Affy.qc<-qc.affy(D, cdfn="DrosGenome1") Error in FUN(c("AFFX-HSAC07/X00351_3_at", "AFFX-HSAC07/X00351_5_at", "AFFX-HSAC07/X00351_M_at", : subscript out of bounds In addition: Warning message: In qc.affy(D, cdfn = "DrosGenome1") : CDF Environment name ' hgu95av2cdf ' does not match cdfname ' drosgenome1cdf ' > D.Affy.qc<-qc.affy(D, cdfn="hgu95av2cdf") Error in FUN(c("AFFX-HSAC07/X00351_3_at", "AFFX-HSAC07/X00351_5_at", "AFFX-HSAC07/X00351_M_at", : subscript out of bounds > D AffyBatch object size of arrays=640x640 features (28 kb) cdf=DrosGenome1 (14010 affyids) number of samples=36 number of genes=14010 annotation=drosgenome1 notes= Any further suggestions would be very appreciated. Also, if you there's any other package that could compute percent present and scale factor for me, that'd do it. With thanks and best wishes Julia
cdf simpleaffy • 598 views