Entering edit mode
Noah Dowell
▴
410
@noah-dowell-3791
Last seen 10.3 years ago
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
