i have two ShortRead object and want write them in two files, but failed > data.class(trinity1) [1] "ShortRead" > data.class(trinity2) [1] "ShortRead" > writeFASTA(trinity1, file="trinity1") Error in for (rec in x) { : invalid for() loop sequence > writeFASTA(trinity2, file="trinity2") Error in for (rec in x) { : invalid for() loop sequence > sessionInfo() R version 2.13.1 (2011-07-08) 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] grid stats graphics grDevices utils datasets methods base other attached packages: [1] ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4 plyr_1.6 [5] ShortRead_1.10.4 Rsamtools_1.4.3 lattice_0.19-30 Biostrings_2.20.4 [9] GenomicRanges_1.4.8 IRanges_1.10.6 loaded via a namespace (and not attached): [1] Biobase_2.12.2 hwriter_1.3 tools_2.13.1 [[alternative HTML version deleted]]

On 11/01/2011 03:49 PM, wang peter wrote: > i have two ShortRead object and want write them in two files, > but failed ShortRead::writeFasta(trinity1, "/tmp/tmp.fa") also Biostrings::write.XStringSet(sread(trinity1), "/tmp/tmp.fa") see > >> data.class(trinity1) > [1] "ShortRead" >> data.class(trinity2) > [1] "ShortRead" >> writeFASTA(trinity1, file="trinity1") > Error in for (rec in x) { : invalid for() loop sequence >> writeFASTA(trinity2, file="trinity2") > Error in for (rec in x) { : invalid for() loop sequence >> sessionInfo() > R version 2.13.1 (2011-07-08) > 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] grid stats graphics grDevices utils datasets methods > base > other attached packages: > [1] ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4 > plyr_1.6 > [5] ShortRead_1.10.4 Rsamtools_1.4.3 lattice_0.19-30 > Biostrings_2.20.4 > [9] GenomicRanges_1.4.8 IRanges_1.10.6 > loaded via a namespace (and not attached): > [1] Biobase_2.12.2 hwriter_1.3 tools_2.13.1 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793