[BioC] chipAlongChrom problem in Ringo

Thu Jan 22 19:22:16 CET 2009

X was created as the following:
MAs <- lapply(RGs, function(thisRG) 
preprocess(thisRG[thisRG$genes$Status=="Probe",],
method="nimblegen", returnMAList=TRUE))
MA <- do.call("rbind", MAs)
X <- asExprSet(MA)
sampleNames(X) <- paste(X$Cy5, X$Feed,sep=".")

> str(probeAnno["5.index"])
 chr [1:21152] "5313_0084_0040" "5313_0760_0290" "5313_0060_0330" ...
> str(probeAnno["5.start"])
 int [1:21152] 3000580 3000665 3000780 3000860 3000975 3001082 3001162 
3001282 3001362 3001462 ...
> str(probeAnno["5.end"])
 int [1:21152] 3000638 3000718 3000837 3000909 3001035 3001138 3001215 
3001339 3001422 3001523 ...
> str(probeAnno["1.index"])
 chr [1:20363] "5313_0105_0555" "5313_0211_0843" "5313_0492_0238" ...
> str(probeAnno["1.start"])
 int [1:20363] 3521489 3521564 3521689 3521764 3521874 3521969 3522064 
3522164 3660593 3660683 ...
> str(probeAnno["1.end"])
 int [1:20363] 3521542 3521613 3521738 3521813 3521923 3522018 3522113 
3522213 3660642 3660732 ...
> str(featureNames(X))
 chr [1:1495582] "MM5000P00314500" "MM5000P00286227" ...
> str(featureNames(X))
 chr [1:1121049] "CHR10FS100018407" "CHR10FS100018507" ...
> featureNames(X)[1:30]
 [1] "CHR10FS100018407" "CHR10FS100018507" "CHR10FS100018612" 
"CHR10FS100018717"
 [5] "CHR10FS100018817" "CHR10FS100018927" "CHR10FS100019007" 
"CHR10FS100019103"
 [9] "CHR10FS100019228" "CHR10FS100019328" "CHR10FS100019428" 
"CHR10FS100019503"
[13] "CHR10FS100019603" "CHR10FS100019703" "CHR10FS100019824" 
"CHR10FS100019927"
[17] "CHR10FS100020027" "CHR10FS100020117" "CHR10FS010119532" 
"CHR10FS010119652"
[21] "CHR10FS010119737" "CHR10FS010119840" "CHR10FS010119947" 
"CHR10FS010120052"
[25] "CHR10FS010120142" "CHR10FS010120232" "CHR10FS010120343" 
"CHR10FS010120453"
[29] "CHR10FS010120552" "CHR10FS010120652"
> str(X)
Formal class 'ExpressionSet' [package "Biobase"] with 6 slots
  ..@ assayData        :<environment: 0x1723efb8>
  ..@ phenoData        :Formal class 'AnnotatedDataFrame' [package 
"Biobase"] with 4 slots
  .. .. ..@ varMetadata      :'data.frame':     8 obs. of  2 variables:
  .. .. .. ..$ varLabel        : Factor w/ 8 levels 
"Cy3","Cy5","DESIGN_NAME",..: 8 5 6 3 7 1 2 4
  .. .. .. ..$ labelDescription: chr [1:8] NA NA NA NA ...
  .. .. ..@ data             :'data.frame':     2 obs. of  8 variables:
  .. .. .. ..$ SlideNumber   : int [1:2] 19657602 20613302
  .. .. .. ..$ FileNameCy3   : chr [1:2] "19657602_532.pair" 
"20613302_532.pair"
  .. .. .. ..$ FileNameCy5   : chr [1:2] "19657602_635.pair" 
"20613302_635.pair"
  .. .. .. ..$ DESIGN_NAME   : chr [1:2] "2007-02-27_MM8_CpG_Island_Pro" 
"2007-02-27_MM8_CpG_Island_Pro"
  .. .. .. ..$ SAMPLE_SPECIES: chr [1:2] "B6" "B6"
  .. .. .. ..$ Cy3           : chr [1:2] "SPF1-input" "GF2-input"
  .. .. .. ..$ Cy5           : chr [1:2] "SPF1-ChIP" "GF1-ChIP"
  .. .. .. ..$ Feed          : chr [1:2] "normFed" "germFree"
  .. .. ..@ dimLabels        : chr [1:2] "sampleNames" "sampleColumns"
  .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] 
with 1 slots
  .. .. .. .. ..@ .Data:List of 1
  .. .. .. .. .. ..$ : int [1:3] 1 1 0
  ..@ featureData      :Formal class 'AnnotatedDataFrame' [package 
"Biobase"] with 4 slots
  .. .. ..@ varMetadata      :'data.frame':     7 obs. of  1 variable:
  .. .. .. ..$ labelDescription: chr [1:7] NA NA NA NA ...
  .. .. ..@ data             :'data.frame':     1121049 obs. of  7 
variables:
  .. .. .. ..$ GENE_EXPR_OPTION: Factor w/ 2 levels "BLOCK1","RANDOM": 1 1 
1 1 1 1 1 1 1 1 ...
  .. .. .. ..$ PROBE_ID        :
 Factor w/ 389307 levels "CHR01FS003521489",..: 225730 225731 225732 225733 
225734 225735 225736 225737 225738 225739 ...
  .. .. .. ..$ POSITION        : int [1:1121049] 100018407 100018507 
100018612 100018717 100018817 100018927 100019007 100019103 100019228 
100019328 ...
  .. .. .. ..$ X               : int [1:1121049] 694 181 365 233 96 314 735 
330 640 379 ...
  .. .. .. ..$ Y               : int [1:1121049] 524 959 429 425 22 286 487 
138 636 11 ...
  .. .. .. ..$ Status          : chr [1:1121049] "Probe" "Probe" "Probe" 
"Probe" ...
  .. .. .. ..$ ID              : chr [1:1121049] "CHR10FS100018407" 
"CHR10FS100018507" "CHR10FS100018612" "CHR10FS100018717" ...
  .. .. ..@ dimLabels        : chr [1:2] "rowNames" "columnNames"
  .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] 
with 1 slots
  .. .. .. .. ..@ .Data:List of 1
  .. .. .. .. .. ..$ : int [1:3] 1 1 0
  ..@ experimentData   :Formal class 'MIAME' [package "Biobase"] with 13 
slots
  .. .. ..@ name             : chr ""
  .. .. ..@ lab              : chr ""
  .. .. ..@ contact          : chr ""
  .. .. ..@ title            : chr ""
  .. .. ..@ abstract         : chr ""
  .. .. ..@ url              : chr ""
  .. .. ..@ pubMedIds        : chr ""
  .. .. ..@ samples          : list()
  .. .. ..@ hybridizations   : list()
  .. .. ..@ normControls     : list()
  .. .. ..@ preprocessing    : list()
  .. .. ..@ other            : list()
  .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] 
with 1 slots
  .. .. .. .. ..@ .Data:List of 1
  .. .. .. .. .. ..$ : int [1:3] 1 0 0
  ..@ annotation       : chr(0)
  ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 
slots
  .. .. ..@ .Data:List of 4
  .. .. .. ..$ : int [1:3] 2 8 1
  .. .. .. ..$ : int [1:3] 2 2 1
  .. .. .. ..$ : int [1:3] 1 1 0
  .. .. .. ..$ : int [1:3] 1 0 0
>
> dim(X)
Features  Samples
 1121049        2

Jianping

--On Thursday, January 22, 2009 6:11 PM +0000 Joern Toedling 
<toedling at ebi.ac.uk> wrote:

>
>
> Jianping Jin wrote:
>> table(probeAnno["5.index"] %in% featureNames(X))
>>
>> FALSE
>> 21152
>
> well, none of the probes seems to be included in the names of the probes
> on your arrays.
> How did you create the object "X"? Can you show me the output of
> str(probeAnno["5.index"])
> str(probeAnno["5.start"])
> str(probeAnno["5.end"])
> ## and for comparison:
> str(probeAnno["1.index"])
> str(probeAnno["1.start"])
>
> # And what is
> str(featureNames(X))
> featureNames(X)[1:30]
> str(X)
> dim(X)
>
>
>>
>> What are feature names in probeAnno? Actually I used a new output file
>> from the script you edited to generate probeAnno with no complain:
>>
>> probeAnno <-
>> posToProbeAnno("C:/from_DriveD/Chip-chip/Bultman/allChromExonerateOut_ne
>> w.txt")
>>
>>    Creating probeAnno mapping for chromosome 1 10 11 12 13 14 15 16 17
>> 18 19 2 3 4 5 6 7 8 9 X Y Done.
>> allChrs <- chromosomeNames(probeAnno)
>> genome(probeAnno) <- "M. musculus (mm9)"
>> arrayName(probeAnno) <- "2007-02-27_MM8_CpG_Island_Pro_Tiling"
>
> This looks alright to me. I think the function is working, but somehow
> the probeAnno does not seem to match your data ExpressionSet.
>
> Maybe can you also provide me with the first few lines of this file,
> just to be sure?
> C:/from_DriveD/Chip-chip/Bultman/allChromExonerateOut_new.txt
>
> Joern

##################################
Jianping Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
Room 3133 Bioinformatics building
CB# 7104, Campus
Phone: (919)843-6105
FAX:   (919)843-3103
E-Mail: jjin at unc.edu