[BioC] Please Help with rMAT: NAs in Enrich Object

Noah Dowell noahd at ucla.edu
Thu Dec 10 02:41:22 CET 2009


Hello All,

I am trying to use the rMAT package to analyze Affymetrix tiling array chip-chip data but have run into some problems that I hope the board can help with.

Up to normalization step looks fine:

> summary(wtAsetNorm)

   Genome interrogated:  Sc03b_MR_v04  
   Chromosome(s) interrogated: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, mitochondrion, plasmid 
   Sample name(s):  WTa WTb input1 input2  
   The total number of probes is:  2643812  
   Preprocessing Information 
     - Transformation: log 
     - Normalization: MAT standardized 

#This is what I used to find enriched regions:

> Enrich  <- callEnrichedRegions(RD, dMax = 75, dMerge = 200, nProbesMin = 8, method = "score", threshold = 1, verbose = FALSE)

#Then after loading the rtracklayer package I start to get some errors that I pasted below:

> genome(Enrich) <- "sacCer2"
> names(Enrich) <- "chrI"
> session <- browserSession("UCSC")
> track(session, "toto") <- Enrich
Error in ucscNormSeqNames(names(from)) : 
  All sequence names should begin with 'chr' or 'scaffold'
> subEnrich <- Enrich[2, ]
> view <- browserView(session, range(subEnrich) * -2)
Error in asMethod(object) : 
  cannot create an IRanges object from an integer vector with missing values
In addition: Warning messages:
1: In min(x, na.rm = na.rm) :
  no non-missing arguments to min; returning Inf
2: In max(x, na.rm = na.rm) :
  no non-missing arguments to max; returning -Inf
3: In .class1(object) : NAs introduced by coercion
Error in ucscForm(range) : 
  error in evaluating the argument 'object' in selecting a method for function 'ucscForm'

#the top of the file looks fine but looking at the tail we see part of the problem:
> tail (Enrich)
RangedData with 6 rows and 1 value column across 18 spaces
        space         ranges |     score
  <character>      <IRanges> | <numeric>
1        <NA> [61862, 61934] | 2.0867882
2        <NA> [63373, 63377] | 1.2274179
3        <NA> [74032, 74443] | 1.3762046
4        <NA> [79253, 80141] | 1.6481782
5        <NA> [80710, 80710] | 0.5607601
6        <NA> [    0,  6261] | 5.9487499



Question:  Where did these NAs come from?  I tried to grep on "chrI" to create a subset lacking the NAs but I think this is a fundamental problem with something I am doing.  Any advice would be appreciated.  Thank you in advance.



Noah Dowell


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