aa<-read.table("") x=as.character(aa[,1]) names(x)=1:length(x) writeFasta(RNAStringSet(x, use.names=TRUE),"miRNA") Error in .Call2("new_XStringSet_from_CHARACTER", classname, elementType, : key 101 not in lookup table R version 2.14.1 (2011-12-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936 [3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936 [4] LC_NUMERIC=C [5] LC_TIME=Chinese (Simplified)_People's Republic of China.936 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ShortRead_1.12.4 latticeExtra_0.6-19 RColorBrewer_1.0-5 Rsamtools_1.6.3 [5] lattice_0.20-0 Biostrings_2.22.0 GenomicRanges_1.6.7 IRanges_1.12.6 [9] biomaRt_2.10.0 loaded via a namespace (and not attached): [1] Biobase_2.14.0 bitops_1.0-4.1 BSgenome_1.22.0 grid_2.14.1 hwriter_1.3 [6] RCurl_1.91-1.1 rtracklayer_1.14.4 tools_2.14.1 XML_3.9-4.1 zlibbioc_1.0.0 -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253

On 03/16/2012 03:21 PM, wang peter wrote: > aa<-read.table("") > x=as.character(aa[,1]) > names(x)=1:length(x) > writeFasta(RNAStringSet(x, use.names=TRUE),"miRNA") > > Error in .Call2("new_XStringSet_from_CHARACTER", classname, elementType, : > key 101 not in lookup table Looks like you are trying to put non-RNA letters into an RNA object: > RNAStringSet("e", use.names=TRUE) Error in .Call2("new_XString_from_CHARACTER", classname, x, start(solved_SEW), : key 101 not in lookup table In BioC devel, the error message also displays the letter associated with the code: > RNAStringSet("accgaggaudnugeacc", use.names=TRUE) Error in .Call2("new_XString_from_CHARACTER", classname, x, start(solved_SEW), : key 101 (char 'e') not in lookup table H. > > R version 2.14.1 (2011-12-22) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 > [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936 > [3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936 > [4] LC_NUMERIC=C > [5] LC_TIME=Chinese (Simplified)_People's Republic of China.936 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ShortRead_1.12.4 latticeExtra_0.6-19 RColorBrewer_1.0-5 > Rsamtools_1.6.3 > [5] lattice_0.20-0 Biostrings_2.22.0 GenomicRanges_1.6.7 > IRanges_1.12.6 > [9] biomaRt_2.10.0 > > loaded via a namespace (and not attached): > [1] Biobase_2.14.0 bitops_1.0-4.1 BSgenome_1.22.0 > grid_2.14.1 hwriter_1.3 > [6] RCurl_1.91-1.1 rtracklayer_1.14.4 tools_2.14.1 > XML_3.9-4.1 zlibbioc_1.0.0 > > > > > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319