Turns out I had the exact same R-devel on my system. And it seems I have the exact same version of the various packages you have and the same search order. On this version, the package vignette works.
So I guess this leaves one of the following possibilities (1) your flyFiles is somehow wrong or (2) withShortRead does not work on your system or (3) bug in Genominator 1.1.6. If I understand you correctly, the exact same code worked yesterday with 1.1.5? I am baffled. I have a hard time seeing how a bug could get introduced that would not also lead to withShortRead failing. So could you send me (off-list) (1) a printing of flyFiles (2) Check that withShortRead works (3) run importFromAlignedReads with verbose = TRUE (4) debug(importToExpData) and step though it. Kasper R version 2.12.0 Under development (unstable) (2010-04-18 r51771) 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] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] yeastRNASeq_0.0.3 ShortRead_1.5.23 Rsamtools_0.2.8 [4] lattice_0.18-5 Biostrings_2.15.27 GenomicRanges_0.1.16 [7] Genominator_1.1.6 GenomeGraphs_1.7.2 biomaRt_2.3.5 [10] IRanges_1.5.79 RSQLite_0.8-4 DBI_0.2-5 loaded via a namespace (and not attached): [1] Biobase_2.7.6 hwriter_1.2 RCurl_1.4-1 tools_2.12.0 XML_2.8-1 On Tue, Apr 20, 2010 at 1:23 PM, joseph franklin <[email protected]> wrote: > Kasper, > Thanks--importing from a vector of filenames was working perfectly. However, > when I upgraded to Genominator 1.1.6 today, and ran the same import command > (I think), I get the error below. > > I may be doing something wrong without realizing it. > Thanks again, > Joe > > (flyFiles is a vector of filenames) > >> flydata<-importFromAlignedReads(x=flyFiles, type="Bowtie" , chrMap=chrMap, >> dbFilename="~/g/annotation/genominator/flydata.db", tablename="raw") > Error in importToExpData(data.frame(chr = chr, location = loc, strand = str), > : > After removing missing locations, df has no rows. > Timing stopped at: 0.94 0.06 0.999 > >> sessionInfo() > R version 2.12.0 Under development (unstable) (2010-04-18 r51771) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] ShortRead_1.5.23 Rsamtools_0.2.8 lattice_0.18-5 > [4] Biostrings_2.15.27 GenomicRanges_0.1.16 Genominator_1.1.6 > [7] GenomeGraphs_1.7.2 biomaRt_2.3.5 IRanges_1.5.79 > [10] RSQLite_0.8-4 DBI_0.2-5 > > loaded via a namespace (and not attached): > [1] Biobase_2.7.6 hwriter_1.2 RCurl_1.4-1 XML_2.8-1 > > > > On 19 Apr 2010, at 11:26, Kasper Daniel Hansen wrote: > >> Hi Joe >> >> This is addressed in the development version. We now have the >> capability of giving importFromAlignedReads a (named) vector of >> filenames instead of a named list of AlignedRead objects. This vector >> of filenames will be read in one at a time, so you just need enough >> memory to process a single lane. I have processed around 160 lanes >> worth of data using this approach. >> >> There is an extended example in the 'with ShortRead' vignette. >> >> importFromAlignedReads also has the capability of directly summing >> several columns (fi you need this). So let us say you have 6 files >> (lanes) and you want to end up with a database with 2 columns >> (assuming you have a 3x2 experiment and you have decided to add up >> over the lanes). Then you can do this using a construction where the >> names of the files are like >> "a", "a", "a", "b", "b", "b" >> (this will create two columns named "a" and "b" each holding 3 lanes >> worth of data). >> >> In this case, all 3 lanes will be read into memory at the same time - >> it is less memory efficient but it was much easier to code. If that >> is impossible you should create a standard 6 column database and then >> use collapseExpData. The importFromAlignedReads is more of a >> convenience (and speed) trick. >> >> I uploaded a new version 1.1.6 yesterday which I recommend, because of >> some documentation updates. This version should replace 1.1.5 on the >> Bioconductor development servers sometime tomorrow. >> >> Kasper >> >> >> On Mon, Apr 19, 2010 at 11:06 AM, joseph franklin >> <[email protected]> wrote: >>> I'm addressing this to Jim Bullard, who has been really helpful answering >>> some of my questions, as well as the list, in case anyone has some advice >>> for me. >>> >>> I've started using Genominator (I'm using the release version right now) to >>> quantitate and analyze RNA-seq data, and have been really successful >>> aggregating AlignedRead objects with my own annotation tables to produce >>> per-gene counts. I've done this with sets of 2-3 AlignedRead objects (each >>> representing an Illumina lane), but I'd like to extend the approach to a >>> few dozen lanes. Since this is far too much data to fit in memory, I need >>> an efficient way to combine many AlignedRead objects at once that doesn't >>> rely on them being loaded as objects at the same time. >>> >>> I imagine that I need to load the objects into tables using the >>> importFromAlignedReads, and then join the appropriate columns, either >>> before or after aggregation (the manual hints that afterwards is >>> preferable). However, there are a few points I'm confused with (probably >>> resulting from my limited experience with SQLite): >>> >>> - I've been unable load to load a SQLite database file that was previously >>> created with the importFromAlignedReads--what is the best way to load the >>> database connection--for instance, during a new R session? >>> >>> -Can AlignedRead objects only be imported (via importFromAlignedReads) as >>> named lists of two or more objects? What about single AlignedRead objects? >>> I would imagine that a solution to my problem would be to create a >>> separate table in a database file for each of my AlignedRead objects (I >>> made a loop to do this), and then join these tables (as long as I can >>> create a connection to the database). >>> >>> I think my problems could be solved if I could load the AlignedRead objects >>> from multiple lanes into tables in database file, load it, and join the >>> appropriate columns from the various tables (and then aggregate with the >>> annotations in a single step--this would seem to be the most >>> straightforward). Any advice on accomplishing these steps would be much >>> appreciated. >>> >>> Thanks again, >>> Joe Franklin >>> >>> ________________________________ >>> Joseph Franklin >>> Department of Cell Biology >>> Yale University >>> 295 Congress Ave, BCMM 137 >>> New Haven, CT 06519 >>> USA >>> >>> _______________________________________________ >>> Bioc-sig-sequencing mailing list >>> [email protected] >>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >>> > > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
