[BioC] R: R: R: R: Probe-level analysis of exon arrays using xps

[cstrato]

Dear Giovanni,

I have just received your mail exactly one minute after sending you the 
explanation for the crash.

 From your newest mail it is clear why you cannot import the expression 
table, since you are using option="probeset" which increases the size of 
the table even further. So to prevent the crash you need to use:
 > data.rma <- rma(data.exon, ..., add.data=FALSE)

Best regards
Christian


On 9/12/11 9:07 PM, Lavorgna Giovanni wrote:
> Dear Christian,
>
> thanks for your answer. Sorry for not being clear in my previous massage. I'll try to clarify things a little bit more.
> The following script running in a R session ( xps_1.12.1 + root 5.27/04) crashes after finishing the rma step, i.e., it completes the line:
>
> rma.ps.core<- rma(data.mix.exon, "MixExonRMAcorePS_prostate_CPU2", filedir=libdir, tmpdir="", background="antigenomic", normalize=TRUE, option="probeset", exonlevel="affx+core")
>
> producing both the correct root and text files,  then hangs and gets killed by the system after memory consumption gets over 90%.
>
>
> ===========================================
> R script
>

snip


>
> ===============================================
>> sessionInfo()
> R version 2.13.1 (2011-07-08)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US       LC_NUMERIC=C         LC_TIME=en_US
>   [4] LC_COLLATE=C         LC_MONETARY=C        LC_MESSAGES=en_US
>   [7] LC_PAPER=en_US       LC_NAME=C            LC_ADDRESS=C
> [10] LC_TELEPHONE=C       LC_MEASUREMENT=en_US LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] xps_1.12.1
>
>
> -----------------------------------------------------------
> Giovanni Lavorgna
> DIBIT-HSR
> Via Olgettina, 58
> 20132 Milan Italy
> Tel: +39-02-2643-4776
> Fax: +39-02-2643-4767
> Email: giovanni.lavorgna  at hsr.it
>
>>
>