DEXSeqHTML won't run - warning message: In is.na(x): is.na() applied to non-(list or vector) or type NULL.
0
0
Entering edit mode
Sam McInturf ▴ 300
@sam-mcinturf-5291
Last seen 8.5 years ago
United States

Hello all,

I am working on a simple DEU case for Arabidopsis and have run into an error with DEXSeqHTML.  Everything runs fine until I try and call DEXSeqHTML on my DEXSeqResults object and I get an error of 

Warning message:
In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'

I looked through the code displayed when calling DEXSeqResults to no avail, and am feeling a bit stuck :/.  Things that may be important; I am using DEXSeq 1.14.1 and R 3.2.0.  No errors occur during the execution of the prior code, although my dispersion failed to fit the normal regression .   My gff was built from the TAIR10_16 release using the HTSeq pipeline provided in the vignette.  Although I did run the dexseq_count.py on each technical replicate, and then summed each tech rep and wrote them to file in a format similar to that of the normal output (no errors so I assume I did this correctly).  As a liner note I will eventually use the individual tech reps but want to get a feel for DEXSeq before implementing the more complex models.  I have not downloaded and run the sample data.

 

Thank you for your time.

Sam

Session Info:

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] DEXSeq_1.14.1             DESeq2_1.8.1              RcppArmadillo_0.5.200.1.0 Rcpp_0.11.6               GenomicRanges_1.20.5     
 [6] GenomeInfoDb_1.4.1        IRanges_2.2.5             S4Vectors_0.6.1           Biobase_2.28.0            BiocGenerics_0.14.0      
[11] BiocParallel_1.2.9       

loaded via a namespace (and not attached):
 [1] genefilter_1.50.0    statmod_1.4.21       locfit_1.5-9.1       reshape2_1.4.1       splines_3.2.0        lattice_0.20-31     
 [7] colorspace_1.2-6     survival_2.38-3      XML_3.98-1.3         foreign_0.8-65       DBI_0.3.1            RColorBrewer_1.1-2  
[13] lambda.r_1.1.7       plyr_1.8.3           stringr_1.0.0        zlibbioc_1.14.0      Biostrings_2.36.1    munsell_0.4.2       
[19] gtable_0.1.2         futile.logger_1.4.1  hwriter_1.3.2        latticeExtra_0.6-26  geneplotter_1.46.0   biomaRt_2.24.0      
[25] AnnotationDbi_1.30.1 proto_0.3-10         acepack_1.3-3.3      xtable_1.7-4         scales_0.2.5         Hmisc_3.16-0        
[31] annotate_1.46.0      XVector_0.8.0        Rsamtools_1.20.4     gridExtra_0.9.1      ggplot2_1.0.1        digest_0.6.8        
[37] stringi_0.5-5        grid_3.2.0           tools_3.2.0          bitops_1.0-6         magrittr_1.5         RCurl_1.95-4.7      
[43] RSQLite_1.0.0        Formula_1.2-1        cluster_2.0.2        futile.options_1.0.0 MASS_7.3-42          rpart_4.1-10        
[49] nnet_7.3-10 

Relevant Code:

Leaf = countFls[7:12]
DescLeaf = sampleDesc[7:12,] #  CS, CST
TissueWiseModel    = ~sample + exon + Treatment:exon
Ldxd = DEXSeqDataSetFromHTSeq(
  countfiles = Leaf,        # vector of count file names
  sampleData = DescLeaf,    # description of said files
  design = TissueWiseModel, # formula for testing
  flattenedfile = gffPath)  # gff used for creating aln files
Ldxd = estimateSizeFactors(Ldxd)
Ldxd = estimateDispersions(Ldxd, BPPARAM=BPPARAM)
Ldxd = testForDEU(Ldxd, BPPARAM=BPPARAM)
Ldxd = estimateExonFoldChanges(Ldxd, fitExpToVar = "Treatment", BPPARAM=BPPARAM)
Ldxr1 = DEXSeqResults(Ldxd)
DEXSeqHTML( object =Ldxr1, FDR=0.05, color=c("#FF000080", "#0000FF80"),BPPARAM=BPPARAM)

 

 
dexseq • 1.8k views
ADD COMMENT
0
Entering edit mode

Hi Sam,

The message that you are getting is a warning not an error, therefore should not stop the code from running.

Do you get an HTML report ?

Alejandro
 

ADD REPLY
0
Entering edit mode

Alejandro,

Thank you for your reply.  I am sorry to say that I missed the fact that the HTML report was generated.  Although something still seems to be wrong.   When looking at the report I can see genes with DEU and when I select a gene the only menu that works is the results option.  Any idea?

Sam

ADD REPLY
0
Entering edit mode

Hi Sam, 

 

I see, these are probably the genes that are producing the warnings. How many samples do you have? Do you get the plot with the normalized counts for these genes?

Alejandro

 

ADD REPLY

Login before adding your answer.

Traffic: 645 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6