Search
Question: plotDEXSeq error in plot.window(xlim = c(0, 1), ylim = c(0, max(matr))) : need finite 'ylim' values
3
gravatar for fizer
9 months ago by
fizer30
US
fizer30 wrote:

Hi,

I am getting an error while plotting dexseq results. I ran dexseq in a very usual way and make good plots but this time I am not sure where and what is wrong with plotting.

 Error in plot.window(xlim = c(0, 1), ylim = c(0, max(matr))) : 
  need finite 'ylim' values In addition: Warning messages:
1: In max(coeff, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
2: In max(matr) : no non-missing arguments to max; returning -Inf

 

  sample run sex age passage rin condition    
1 Sample_18 new M 64 5 6.9 control    
2 Sample_206 new F 49 2 7.4 control    
3 Sample_271 new F 26 2 8 control    
4 Sample_272 new F 24 2 6.9 control    
5 Sample_277 new M 23 2 6.9 control    
6 Sample_53 new F 24 2 8 control    
7 Sample_16 new F 32 2 10 patient    
8 Sample_180 new M 22 4 7.4 patient    
9 Sample_251 new M 22 2 10 patient    
10 Sample_261 new M 37 2 9.2 patient    
11 Sample_269 new F 41 2 7.4 patient    
12 Sample_270 new F 39 2 9.3 patient    
13 Sample_275 new F 26 2 9.7 patient    
14 Sample_32 new F 25 2 8.8 patient    
15 Sample_92 new M 40 2 9.7 patient    
fullmodel= ~ sample + exon + exon:age + exon:sex + exon:passage + exon:condition 
reduced_model = ~ sample + exon + exon:age + exon:sex + exon:passage

dxd = DEXSeqDataSet(counts.filt, sampleData= coldata, groupID = gID, featureID = fID, design= fullmodel)
dxd = estimateSizeFactors(dxd)
dxd = estimateDispersions(dxd, BPPARAM = BP, formula = fullmodel)
dxd = testForDEU(dxd, BPPARAM=BPPARAM, fullModel = fullmodel, reducedModel = reduced_model)
dxd = estimateExonFoldChanges(dxd, fitExpToVar="condition", BPPARAM = BPPARAM)
dxr = DEXSeqResults(dxd)

Following is how my results object look. I got 164 significant DEXs from my data (p < 0.05): 

LRT p-value: full vs reduced

DataFrame with 233132 rows and 12 columns
                            groupID   featureID exonBaseMean  dispersion         stat    pvalue      padj   control       patient
                        <character> <character>    <numeric>   <numeric>    <numeric> <numeric> <numeric> <numeric> <numeric>
ENSG00000000003:001 ENSG00000000003         001     705.8388 0.002036784 0.9374992252 0.3329218 0.7906055  34.01570  34.46083
ENSG00000000003:002 ENSG00000000003         002     329.1962 0.001544407 2.5335265978 0.1114509 0.6094709  24.22142  24.68291
...                             ...         ...          ...         ...          ...       ...       ...       ...       ...
ENSG00000273486:001 ENSG00000273486         001     25.77248          NA           NA        NA        NA        NA        NA
ENSG00000273489:001 ENSG00000273489         001    125.03100          NA           NA        NA        NA        NA        NA
                    log2fold_patient_control   genomicData       countData
                               <numeric> <GRangesList>        <matrix>
ENSG00000000003:001          0.018756457               491:748:798:...
ENSG00000000003:002          0.027229156               229:325:370:...
...                                  ...           ...             ...
ENSG00000273486:001                   NA                  24:17:37:...
ENSG00000273489:001                   NA               223:275:118:...

 

I went on to see plotDEXSeq code to debug the error and got a new error:

 Error in vst(coeff, object) : less than 'nsub' rows,
  it is recommended to use varianceStabilizingTransformation directly 

 

Has anybody every faced this error.

 

 

I am also attaching the sessionInfo() below;

R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DEXSeq_1.20.1              RColorBrewer_1.1-2         BiocParallel_1.8.1         splitstackshape_1.4.2     
 [5] data.table_1.10.0          reshape2_1.4.2             VennDiagram_1.6.17         futile.logger_1.4.3       
 [9] GenomicFeatures_1.26.2     gridExtra_2.2.1            plyr_1.8.4                 tidyr_0.6.1               
[13] org.Hs.eg.db_3.4.0         AnnotationDbi_1.36.1       GOSemSim_2.0.4             ggplot2_2.2.1             
[17] gplots_3.0.1               DESeq2_1.14.1              SummarizedExperiment_1.4.0 Biobase_2.34.0            
[21] GenomicRanges_1.26.2       GenomeInfoDb_1.10.2        IRanges_2.8.1              S4Vectors_0.12.1          
[25] BiocGenerics_0.20.0       

loaded via a namespace (and not attached):
 [1] splines_3.3.1            gtools_3.5.0             Formula_1.2-1            assertthat_0.1          
 [5] statmod_1.4.27           latticeExtra_0.6-28      Rsamtools_1.26.1         RSQLite_1.1-2           
 [9] backports_1.0.5          lattice_0.20-34          digest_0.6.11            XVector_0.14.0          
[13] checkmate_1.8.2          colorspace_1.3-2         htmltools_0.3.5          Matrix_1.2-8            
[17] XML_3.98-1.5             biomaRt_2.30.0           genefilter_1.56.0        zlibbioc_1.20.0         
[21] xtable_1.8-2             GO.db_3.4.0              scales_0.4.1             gdata_2.17.0            
[25] htmlTable_1.8            tibble_1.2               annotate_1.52.1          nnet_7.3-12             
[29] lazyeval_0.2.0           survival_2.40-1          magrittr_1.5             memoise_1.0.0           
[33] hwriter_1.3.2            foreign_0.8-67           tools_3.3.1              stringr_1.1.0           
[37] munsell_0.4.3            locfit_1.5-9.1           cluster_2.0.5            lambda.r_1.1.9          
[41] Biostrings_2.42.1        caTools_1.17.1           RCurl_1.95-4.8           bitops_1.0-6            
[45] base64enc_0.1-3          labeling_0.3             gtable_0.2.0             DBI_0.5-1               
[49] R6_2.2.0                 GenomicAlignments_1.10.0 knitr_1.15.1             dplyr_0.5.0             
[53] rtracklayer_1.34.1       Hmisc_4.0-2              futile.options_1.0.0     KernSmooth_2.23-15      
[57] stringi_1.1.2            Rcpp_0.12.9              geneplotter_1.52.0       rpart_4.1-10            
[61] acepack_1.4.1

 

ADD COMMENTlink modified 9 months ago • written 9 months ago by fizer30

Hi 

Could you include the code that you used to call plotDEXSeq? Does this happen for all the genes or only for a couple of genes?

Alejandro

ADD REPLYlink written 9 months ago by Alejandro Reyes1.5k
2

Hi Alejandro,

I am experiencing the same error. I don't know if @fizer has noticed this (and this is true for me), that the genomicData column contains no values. Could this be that the reads fail to "map" because of this loss of genomic information?

-Blair

ADD REPLYlink written 7 months ago by bojingjia20
1

Hi Blair. If you don't specify a gtf file or genomic coordinates when you generate your DEXSeqDataSet object, the genomicData slot will be empty. Did you specify genomic coordinates?

Alejandro

ADD REPLYlink written 7 months ago by Alejandro Reyes1.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 133 users visited in the last hour