[BioC] Ringo package: error using computeRunningMedians function
Diego Villar
dvillar at iib.uam.es
Mon Aug 31 18:33:28 CEST 2009
Dear Joern,
I looked at the output of the commands you suggested (in some instances
only a fragment of the output is copied):
table(ProbeAnno["11.unique"])
0
16314
table(ProbeAnno["11.index"])
chr11.990402.990462 chr11.990469.990529
chr11.990589.990649
1 1
1
chr11.990598.990658 chr11.99098574.99098634
chr11.99098696.99098756
1 1
1
chr11.99191352.99191412 chr11.99191505.99191565
chr11.99191589.99191649
1 1
1
chr11.992384.992444 chr11.992475.992535
chr11.992519.992579
1 1
1
chr11.992572.992632 chr11.992617.992677
chr11.99265506.99265566
1 1
1
chr11.99265661.99265721 chr11.99272465.99272525
chr11.99272618.99272678
1 1
1
chr11.99272726.99272786 chr11.99272763.99272823
chr11.99303967.99304027
1 1
1
chr11.99304052.99304112 chr11.99304124.99304184
chr11.99304202.99304262
1 1
1
chr11.99484048.99484108 chr11.99484323.99484383
chr11.997710.997770
1 1
1
chr11.997821.997881 chr11.997916.997976
chr11.997947.998007
1 1
1
chr11.998012.998072 chr11.998109.998169
chr11.998156.998216
1 1
1
chr11.998214.998274 chr11.998281.998341
chr11.998364.998424
1 1
1
featureNames(eSet)
[93143] "chr14.103260174.103260234" "chr15.49420957.49421017"
[93145] "chr10.121418721.121418781" "chr3.142475706.142475766"
[93147] "chr12.4750441.4750501" "chr19.60858191.60858251"
[93149] "chr19.12836986.12837046" "chr2.74610106.74610166"
[93151] "chr3.15030218.15030278" "chr4.3302037.3302097"
[93153] "chr12.6816461.6816521" "chr16.87787089.87787149"
[93155] "chr9.136846349.136846409" "chr14.104905960.104906020"
[93157] "chr15.88609844.88609904" "chr19.16097255.16097315"
[93159] "chrX.23302155.23302215" "chr22.36928650.36928710"
[93161] "chr21.46801174.46801234" "chr1.54802941.54803001"
[93163] "chr5.71439940.71440000" "chr13.20109437.20109497"
[93165] "chr17.19221465.19221525" "chr15.41265439.41265499"
[93167] "chr17.40674754.40674814" "chr9.132028622.132028682"
[93169] "chr5.137749901.137749961" "chr2.74916286.74916346"
[93171] "chr12.119485201.119485261" "chr1.2021070.2021130"
[93173] "chr11.118460384.118460444" "chr9.139292058.139292118"
[93175] "chr16.53916013.53916073" "chr14.58726017.58726077"
[93177] "chr1.95355225.95355285" "chr20.35407771.35407831"
[93179] "chr9.136391391.136391451" "chr17.53678992.53679052"
[93181] "chr7.75447663.75447723" "chr3.141175234.141175294"
[93183] "chr20.30850078.30850138" "chr17.40681467.40681527"
[93185] "chr20.29657541.29657601" "chr7.156895220.156895280"
[93187] "chr12.51631466.51631526" "chr19.3086743.3086803"
Checking on the error as you indicated I retrieve the following values:
smoothX <- computeRunningMedians(eSet, probeAnno=ProbeAnno,
+ modColumn = "Cy5", winHalfSize = 400)
Chromosome 1 ...
170809ds ... 261108no ...
Chromosome 10 ...
170809ds ... 261108no ...
Chromosome 11 ...
170809ds ... Error en newExprs[chridx, i] <- chrrm :
NAs no son permitidos en asignaciones subscritas
Enter a frame number, or 0 to exit
1: computeRunningMedians(eSet, probeAnno = ProbeAnno, modColumn =
"Cy5", winHa
Selección: 1
Called from: eval(expr, envir, enclos)
Browse[1]> str(chridx)
int [1:16314] 40027 121370 99412 63143 131069 125479 54552 32661 81358
80190 ...
Browse[1]> str(i)
int 1
Browse[1]> str(chrrm)
Named num [1:16314] NA NA NA NA 0.164 ...
- attr(*, "names")= chr [1:16314] "186594" "186802" "186874"
"186940" ...
Thanks,
Diego
Con fecha 31/8/2009, "Joern Toedling" <Joern.Toedling at curie.fr>
escribió:
>Well, this looks all fine to me. I cannot tell you immediately where the
>problem is, and since I have not run into such an error before, we'll have to
>search for the source of the problem together. The fact that chromosomes 1 and
>10 work but chromosome 11 does not strongly suggests that there is something
>unusual with the elements of that chromosome 11 in the probeAnno object.
>
>Further things we can check:
>table(ProbeAnno["11.unique"])
>table(ProbeAnno["11.index"] %in% featureNames(eSet))
>
>Otherwise, consider setting
>options(error=recover)
>then when the error occurs, type the frame number of'computeRunningMedians'
>and please tell me what the result of
>str(chridx)
>str(i)
>str(chrrm)
>are.
>Alternatively, if you don't mind you could save the objects eSet and ProbeAnno
>into a file (using command 'save') and provide them somewhere to me for
>downloading. I could check these things myself then.
>
>Regards,
>Joern
>
>
>On Mon, 31 Aug 2009 14:55:41 +0000, Diego Villar wrote
>> 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
>>
>> 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
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