Dear List, I have tried to calculate "ai" by commands bellow, but warning returns. Is my ai calculated correctly? or do I have to calculate again by using 'complement(DNAStringSet(seq))'. If I have to calculate again with 'complement(DNAStringSet(seq))', how can I done that ? Thanks. > ai <- compute.affinities.local(data, Array=NULL) Computing affinities..............................Done. Warning message: 'complementSeq' is deprecated. Use 'complement(DNAStringSet(seq))' instead. See '?complementSeq' > data AffyBatch object size of arrays=712x712 features (14 kb) cdf=Zebrafish (15617 affyids) number of samples=30 number of genes=15617 annotation=zebrafish notes= Naok

This is looking like a minor problem in gcRMA, as its code does not reflect recent changes in Biostrings. The warning just informs you that the function complementSeq will be removed in the near future. You can otherwise proceed with the results obtained. L. Naoki Irie wrote: > Dear List, > > > I have tried to calculate "ai" by commands bellow, but warning returns. > Is my ai calculated correctly? or do I have to calculate again by using > 'complement(DNAStringSet(seq))'. > If I have to calculate again with 'complement(DNAStringSet(seq))', how > can I done that ? > > Thanks. > > > > ai <- compute.affinities.local(data, Array=NULL) > Computing affinities..............................Done. > Warning message: > 'complementSeq' is deprecated. > Use 'complement(DNAStringSet(seq))' instead. > See '?complementSeq' > > > data > AffyBatch object > size of arrays=712x712 features (14 kb) > cdf=Zebrafish (15617 affyids) > number of samples=30 > number of genes=15617 > annotation=zebrafish > notes= > > > Naok > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor