On 03/04/2011 10:10 AM, Sean Davis wrote: > On Mar 4, 2011 11:15 AM, "kirti prakash" <[email protected]> wrote: >> >> Hi, >> >> I wanted to get fastq files associated with some SRA >> >> So I was going through the following SRAdb vignettes >> > http://bioconductor.org/packages/2.6/bioc/vignettes/SRAdb/inst/doc/SRAdb.pdf >> >> < > http://bioconductor.org/packages/2.6/bioc/vignettes/SRAdb/inst/doc/SRAdb.pdf >> I >> am able to run most of the commands except the ones in section 3.5(which I >> actually need) >> >> The error I am getting is >> getFastq (in_acc=c("SRR000648","SRR000657"), sra_con=sra_con, >> destdir=getwd()) >> Error: could not find function "getFastq" >> >> getFastq >> Error: object 'getFastq' not found >> >> Similarly for listFastq and getFastInfo functions >> >> I am wondering if I am missing something ? > > Unfortunately, you are not. NCBI has removed the fastq files from its site, > so these functions have been removed from sraDB.
Also, I think your version of R and SRAdb don't match (biocLite installed SRAdb version 1.2.1 under R-2.11.1). A better bet is to update to R-2.12.2, update your installed packages http://bioconductor.org/install/ and use the current vignette, available with browseVignettes("SRAdb") This won't make getFastq magically appear, but it will make the software and vignette function in a consistent way. Martin > > Sean > >> Best regards, >> >> Kirti Prakash >> >> sessionInfo() >> R version 2.11.1 (2010-05-31) >> x86_64-unknown-linux-gnu >> >> locale: >> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C >> [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.iso885915 >> [7] LC_PAPER=en_US.iso885915 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] SRAdb_1.4.1 graph_1.28.0 RSQLite_0.9-2 DBI_0.2-5 >> >> loaded via a namespace (and not attached): >> [1] Biobase_2.8.0 GEOquery_2.16.3 RCurl_1.4-3 tools_2.11.1 >> [5] XML_3.1-0 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
