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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