On 02/01/2011 11:08 AM, Kunbin Qu wrote: > Hi, all: > > I am trying to assess the read quality score for each lane (mean and median etc.) from a Hi-Seq run which has about 70-90 million reads per lane. When I used as(quality(readFastQ), "numeric"), it gave an error "allocMatrix: too many elements specified". Is there a way to get around this? Thanks.
An R vector (including a matrix) must be less than 2^31-1 elements long, so a work-around is to divide the ShortReadQ object into chunks such that sum(width(s1q)) < 2^31-1. Depending on what you do down-stream, it might be sufficient to use alphabetByCycle (alphabet use epr cycle) or alphabetFrequency (alphabet use per read). Martin > > -Kunbin> > >> seqQ > class: ShortReadQ > length: 76115764 reads; width: 50 cycles >> s1q<-quality(seqQ) >> s1q > class: SFastqQuality > quality: > A BStringSet instance of length 76115764 > width seq > [1] 50 aa``_BcccccccccddddddadJdQTTTB]]SZY[\_PZbc_bbddad\ > [2] 50 ]\SUTB_[[][]]]]dfecfef^cddffcedbd^ddeed`cd`dedeef` > [3] 50 aa```Bcccb\ccccggggggggegegefgggege^abbdeeabedgade > [4] 50 ^VZXWB_YN]TMUTYddadd_dcda[[R[T\``Wc^bc\bacaddd`a\d > [5] 50 cccccBc]cacbb]cgggdfggegegaggeeggggaeegggbecgefcZ\ > [6] 50 ddccdbeeea_]]`Z\cc`c]SZ_]]S[K]ccbbWaTL_``V]^_cddWV > [7] 50 XYWWYB[]_]]]^\]cddddbfedfdddbacacacfff_edTd`aU[XYX > [8] 50 bbb`bBcccccddddgggggggggggegggfggdgggggegeggdggggg > [9] 50 bba`bBcccccddddgeggegggggdggffggcfe`edeegae`geddd` > ... ... ... > [76115756] 50 e`eeeBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB > [76115757] 50 aaVa`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB > [76115758] 50 ]ZXRERHZZFUZ[XDKKDDRHLPUQa```^XZ^HQ`]]T[WDXRH^YSWW > [76115759] 50 eeededd_dcBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB > [76115760] 50 c[^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB > [76115761] 50 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB > [76115762] 50 __BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB > [76115763] 50 _^X_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB > [76115764] 50 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB >> summary(as(s1q, "numeric")) > Error in asMethod(object) : allocMatrix: too many elements specified >> sessionInfo() > R version 2.11.0 (2010-04-22) > 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] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ShortRead_1.6.2 Rsamtools_1.0.1 lattice_0.19-11 > [4] Biostrings_2.16.7 GenomicRanges_1.0.1 IRanges_1.6.8 > > loaded via a namespace (and not attached): > [1] Biobase_2.8.0 grid_2.11.0 hwriter_1.3 tools_2.11.0 >> > > > ______________________________________________________________________ > The contents of this electronic message, including any attachments, are > intended only for the use of the individual or entity to which they are > addressed and may contain confidential information. If you are not the > intended recipient, you are hereby notified that any use, dissemination, > distribution, or copying of this message or any attachment is strictly > prohibited. If you have received this transmission in error, please send an > e-mail to [email protected] and delete this message, along with > any attachments, from your computer. > [[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
