[BioC] Ringo package: error using computeRunningMedians function

[Diego Villar]

Hello, Joern:

  Thanks a lot for your prompt reply.

*** How did you build the probeAnno object? ***

  I build the ProbeAnno object from a table resembling a pos file, using
 the following:

ProbeAnno<- posToProbeAnno("alt_prom_array.pos", chrNameColumn =
"CHROMOSOME",
   probeColumn = "Name", chrPositionColumn = "POSITION",
   lengthColumn = "LENGTH", sep="\t", genome="H.Sapiens (hg17)",
   microarrayPlatform="Agilent alt prom array (custom)")

The pos file I used is a tab delimited text file which looks like:

Name	ID	CHROMOSOME	POSITION	COUNT	LENGTH
chrX.71280574.71280634	FLJ44635_71280558_16	chrX	71280574	1	60
chr10.116034763.116034823	VWA2_116034286_477	chr10	116034763	1	60
chr11.383389.383449	PKP3_383245_144	chr11	383389	1	60

I built it this way since the array is an old Agilent custom array (hg17)
and the function that you propose in the Ringo script for creating a
probeAnno object from the genes section of an RG did not work on my data.

The probeAnno generated in this way works fine with chipAlongChrom
function on a region of chromosome 11, but after that I get the
mentioned error when using computeRunningMedians.

chipAlongChrom(eSet, chrom="11", xlim=c(18371851,18373350),
               ylim=c(-2,4), probeAnno=ProbeAnno, gff=gff)

smoothX <- computeRunningMedians(eSet, probeAnno=ProbeAnno,
modColumn = "Cy5", winHalfSize = 400)

*** Assuming your probeAnno object is called P,what is the output of
validObject(P), str(P["11.start"]) str(P["11.index"])? ***

> validObject(ProbeAnno)
[1] TRUE
> str(ProbeAnno["11.start"])
 int [1:16314] 186565 186773 186844 186910 189356 189422 189471 189516
189604 279308 ...
> str(ProbeAnno["11.index"])
 chr [1:16314] "chr11.186565.186625" "chr11.186773.186833" ...

*** And please always remember to add the result of typing
"sessionInfo()" in
your R to any question you ask on this list, as this allows us to see
which
software versions you are using ***

> sessionInfo()
R version 2.9.0 (2009-04-17)
i386-pc-mingw32

locale:
LC_COLLATE=Spanish_Spain.1252;LC_CTYPE=Spanish_Spain.1252;LC_MONETARY=Spanish_Spain.1252;LC_NUMERIC=C;LC_TIME=Spanish_Spain.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Ringo_1.8.0        Matrix_0.999375-24 lattice_0.17-22    limma_2.18.2
[5] RColorBrewer_1.0-2 Biobase_2.4.1

loaded via a namespace (and not attached):
 [1] annotate_1.22.0     AnnotationDbi_1.6.0 DBI_0.2-4
 [4] genefilter_1.24.0   grid_2.9.0          RSQLite_0.7-1
 [7] splines_2.9.0       survival_2.35-4     tools_2.9.0
[10] xtable_1.5-5

Thanks again for your help,

              Diego





Con fecha 31/8/2009, "Joern Toedling" <Joern.Toedling at curie.fr>
escribió:

>Hello,
>
>I'm afraid I do not understand the error message. NAs in your ExpressionSet
>should not be a problem. I suspect that the problem might be with your
>probeAnno object, especially with the probes on chromosome 11 (since it seems
>to work with chromosomes 1 and 10). How did you build the probeAnno object?
>Assuming your probeAnno object is called P,
>what is the output of
>validObject(P)
>str(P["11.start"])
>str(P["11.index"])
>? And please always remember to add the result of typing "sessionInfo()" in
>your R to any question you ask on this list, as this allows us to see which
>software versions you are using.
>
>Regards,
>Joern
>
>On Mon, 31 Aug 2009 11:48:17 +0000, Diego Villar wrote
>> Dear All,
>>
>>   I am trying to use Ringo for analysis of Agilent platform ChIP-
>> chip. I get the following output/error when applying the computeRunningMedians
>> function to my expression set (2 samples, one normal and one dye-
>> swap):
>>
>>   Chromosome 1 ...
>> 170809ds ... 261108no ...
>> Chromosome 10 ...
>> 170809ds ... 261108no ...
>> Chromosome 11 ...
>> 170809ds ... Error en newExprs[chridx, i] <- chrrm :
>>   NAs are not allowed in subscribed assignations
>>
>>    Does this mean missing values are not allowed at all for this
>> function? How could I modify my input so that the function would
>> work on my data? Would I need to substite NAs somehow in the ExpressionSet?
>>
>>    Thanks in advance for your time and help,
>>
>>                 Diego Villar
>>
>
>
>---
>Joern Toedling
>Institut Curie -- U900
>26 rue d'Ulm, 75005 Paris, FRANCE
>Tel. +33 (0)156246926
>

           Diego Villar
           Laboratorio 2.5.2
           Teléfono 915854442
           Instituto de Investigaciones Biomédicas     "Alberto Sols"
           CArturo Duperier, 4 28029 Madrid