[BioC] xps and unifilter; Error: UnitID not found; error in function ‘ExportData’

[cstrato]

Dear John,

I assume that you did "rma(data.exon,...,option="probeset",...)", is 
this correct?

The reason for my question is that I have just tested function 
"unifilter()" for the results of rma(...,option="transcript",...) and 
rma(...,option="probest",...). In the first case function unifilter() is 
ok, however, for the second case I can reproduce the error you get. Thus 
I need to investigate and will let you know.

Best regards
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
_._._._._._._._._._._._._._._._._._


On 6/18/10 10:57 AM, John Coulthard wrote:
>
> Dear list
>
> Can anyone enlighten me to the meaning of this error and how I might get round it?
>
>> rma.ufr<- unifilter(data.rma, ...)
>
> Error: UnitID<322394>  not found.
>
> An error has occured: Need to abort current process.
>
> Error in .local(object, ...) : error in function ‘ExportData’
>
>
> More details below
>
> Thanks
> John
>
>> unifltr<- UniFilter(unitest=c("t.test","two.sided","none",0,0.0,FALSE,0.95,TRUE),foldchange=c(1.3,"both"),unifilter=c(0.1,"pval"))
>> rma.ufr<- unifilter(data.rma, filename="tmpdt_TestUnifilter", filedir=getwd(), filter=unifltr, group = c("a242", "g8", "g8", "g8", "a242", "a242", "g8", "g8", "g8", "a242", "a242", "a242"), verbose = T)
> Opening file</home/Data/PHD1/HuEx-1_0-st-v2.root>  in<READ>  mode...
> Creating new temporary file</home/ann/Data/PHD1/tmpdt_TestUnifilter_ufr_20100618_95439.root>...
> Opening file</home/Data/PHD1/tmpdt_TestRMA_20100618_74202.root>  in<READ>  mode...
> Unifilter:<32235>  genes of<1386572>  genes fulfill filter criteria.
> Opening file</home/Data/PHD1/HuEx-1_0-st-v2.root>  in<READ>  mode...
> Opening file</home/Data/PHD1/tmpdt_TestUnifilter_ufr_20100618_95439.root>  in<READ>  mode...
> Opening file</home/Data/PHD1/tmpdt_TestUnifilter_ufr_20100618_95439.root>  in<READ>  mode...
> Exporting data from tree<UniTest>  to file</home/Data/PHD1/tmpdt_TestUnifilter_ufr_20100618_95439.txt>...
> Error: UnitID<322394>  not found.
> An error has occured: Need to abort current process.
> Error in .local(object, ...) : error in function ‘ExportData’
>
>> class(data.rma)
> [1] "ExprTreeSet"
> attr(,"package")
> [1] "xps"
>> summary(data.rma)
>       Length       Class        Mode
>            1 ExprTreeSet          S4
>> sessionInfo()
> R version 2.11.0 (2010-04-22)
> i386-redhat-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] xps_1.8.0
>
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