Please Help with rMAT: NAs in Enrich Object
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Noah Dowell ▴ 410
@noah-dowell-3791
Last seen 9.5 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
Normalization Preprocessing rtracklayer IRanges rMAT Normalization Preprocessing IRanges • 1.1k views
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@martin-morgan-1513
Last seen 4 weeks ago
United States
Hi Noah -- Noah Dowell wrote: > 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" Perhaps it is related to > x=RangedData(IRanges(1, 1:3), space=c(1,1,2)) > names(x) = "chrI" > x RangedData with 3 rows and 0 value columns across 2 spaces space ranges | <character> <iranges> | 1 chrI [1, 1] | 2 chrI [1, 2] | 3 <na> [1, 3] | which introduces NA into 'space'. Maybe (though not quite -- mitochrion and plasmid need to be renamed or removed) > x=RangedData(IRanges(1, 1:3), space=c(1,1,2)) > names(x) = paste("chr", as.roman(names(x)), sep="") > x RangedData with 3 rows and 0 value columns across 2 spaces space ranges | <character> <iranges> | 1 chrI [1, 1] | 2 chrI [1, 2] | 3 chrII [1, 3] | ? Martin >> 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 > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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