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.

-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
>


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