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Question: DEXSeqHTML doesn't creates plots
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gravatar for Assa Yeroslaviz
2.0 years ago by
Assa Yeroslaviz1.3k
Munich, Germany
Assa Yeroslaviz1.3k wrote:

Hi,

 

I am trying to export the html file for the DEXSeq results, but keep getting a warning message, when running DEXSeqHTML.

here is the script I am running:

CR4W0h.CTRL0hdxd <- DEXSeqDataSetFromHTSeq(CR4W0h.CTRL0hfiles,
                                           sampleData = CR4W0h.CTRL0hsampleTable,
                                           design = ~sample + exon + treatment:exon,
                                           flattenedfile = flattenedFile)

CR4W0h.CTRL0hdxd <- CR4W0h.CTRL0hdxd[1:1000,] # subsetting the data

CR4W0h.CTRL0hdxd <- estimateDispersions(CR4W0h.CTRL0hdxd, BPPARAM = BPPARAM)
CR4W0h.CTRL0hdxd = testForDEU( CR4W0h.CTRL0hdxd,  BPPARAM = BPPARAM)CR4W0h.CTRL0hdxd = estimateExonFoldChanges( CR4W0h.CTRL0hdxd, fitExpToVar="treatment", BPPARAM = BPPARAM)
CR4W0h.CTRL0hdxr = DEXSeqResults( CR4W0h.CTRL0hdxd )

#export the counts for each exon in a table:
## read counts
dir.create("A1.CR4W0h.CTRL0h")
genemap <- getBM( attributes = c("ensembl_gene_id", "entrezgene", "mgi_id", "mgi_symbol", "external_gene_name"),
                  filters = "ensembl_gene_id",
                  values = as.character(unique(CR4W0h.CTRL0hdxr$groupID)),
                  mart = ensembl )
row.names(genemap) <- genemap[,1]

## export the html for the sig. deregulated exons/genes
DEXSeqHTML(CR4W0h.CTRL0hdxr , FDR=.99, color=c("#00CC00", "#FF0000"),file = "A1.CR4W0h.CTRL0h.html", path = "A1.CR4W0h.CTRL0h", extraCols= genemap, BPPARAM = BPPARAM)
Warning message:
In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'

I get the html file and the folder with the images, but there are no plots there.

(The FDR is set to 0.9, because I am using a subset of my data (first 1000 genes in the dxd object) to speed up the testing.)

Is there any reason, why I don't get the plots of normalized counts?

thanks

Assa

Below is some info about the dxr object:

> names(CR4W0h.CTRL0hdxr)
 [1] "groupID"             "featureID"           "exonBaseMean"       
 [4] "dispersion"          "stat"                "pvalue"             
 [7] "padj"                "CR4Wo"               "ctrl"               
[10] "log2fold_ctrl_CR4Wo" "genomicData"         "countData"          
[13] "transcripts

> head(CR4W0h.CTRL0hdxr)

LRT p-value: full vs reduced

DataFrame with 6 rows and 13 columns
                                   groupID   featureID exonBaseMean  dispersion
                               <character> <character>    <numeric>   <numeric>
ENSMUSG00000000001:E001 ENSMUSG00000000001        E001    55.190150 0.006387267
ENSMUSG00000000001:E002 ENSMUSG00000000001        E002     9.096948 0.006822635
ENSMUSG00000000001:E003 ENSMUSG00000000001        E003     7.069048 0.010276909
ENSMUSG00000000001:E004 ENSMUSG00000000001        E004    10.239692 0.005841850
ENSMUSG00000000001:E005 ENSMUSG00000000001        E005     6.997248 0.008234490
ENSMUSG00000000001:E006 ENSMUSG00000000001        E006     9.971844 0.014578142
                              stat     pvalue      padj     CR4Wo      ctrl
                         <numeric>  <numeric> <numeric> <numeric> <numeric>
ENSMUSG00000000001:E001 1.94426740 0.16320593 0.9866054 13.254746 14.010069
ENSMUSG00000000001:E002 0.03265748 0.85659221 0.9911929  5.889862  5.807485
ENSMUSG00000000001:E003 0.12982024 0.71861849 0.9911929  5.278806  5.063725
ENSMUSG00000000001:E004 0.13516393 0.71313686 0.9911929  6.242174  6.037368
ENSMUSG00000000001:E005 3.15406029 0.07573829 0.9866054  5.668869  4.499273
ENSMUSG00000000001:E006 0.43437184 0.50985151 0.9911929  5.818799  6.325129
                        log2fold_ctrl_CR4Wo                genomicData
                                  <numeric>                  <GRanges>
ENSMUSG00000000001:E001          0.07995509 3:-:[108107280, 108109316]
ENSMUSG00000000001:E002         -0.02032015 3:-:[108109403, 108109612]
ENSMUSG00000000001:E003         -0.06001257 3:-:[108111935, 108112088]
ENSMUSG00000000001:E004         -0.04812888 3:-:[108112473, 108112602]
ENSMUSG00000000001:E005         -0.33336897 3:-:[108115763, 108115891]
ENSMUSG00000000001:E006          0.12037342 3:-:[108118301, 108118458]
                        countData transcripts
                        <integer>      <list>
ENSMUSG00000000001:E001        53    ########
ENSMUSG00000000001:E002        14    ########
ENSMUSG00000000001:E003        11    ########
ENSMUSG00000000001:E004        10    ########
ENSMUSG00000000001:E005        14    ########
ENSMUSG00000000001:E006        15    ########

 

 

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] 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
[8] methods   base     

other attached packages:
 [1] DEXSeq_1.16.2              DESeq2_1.10.0             
 [3] RcppArmadillo_0.6.200.2.0  Rcpp_0.12.2               
 [5] SummarizedExperiment_1.0.1 GenomicRanges_1.22.1      
 [7] GenomeInfoDb_1.6.1         IRanges_2.4.4             
 [9] S4Vectors_0.8.3            Biobase_2.30.0            
[11] BiocGenerics_0.16.1        BiocParallel_1.4.0        

loaded via a namespace (and not attached):
 [1] genefilter_1.52.0    statmod_1.4.22       locfit_1.5-9.1      
 [4] reshape2_1.4.1       splines_3.2.2        lattice_0.20-33     
 [7] colorspace_1.2-6     survival_2.38-3      XML_3.98-1.3        
[10] foreign_0.8-66       DBI_0.3.1            RColorBrewer_1.1-2  
[13] lambda.r_1.1.7       plyr_1.8.3           stringr_1.0.0       
[16] zlibbioc_1.16.0      Biostrings_2.38.2    munsell_0.4.2       
[19] gtable_0.1.2         futile.logger_1.4.1  hwriter_1.3.2       
[22] latticeExtra_0.6-26  geneplotter_1.48.0   biomaRt_2.26.0      
[25] AnnotationDbi_1.32.0 proto_0.3-10         acepack_1.3-3.3     
[28] xtable_1.8-0         scales_0.3.0         Hmisc_3.17-0        
[31] annotate_1.48.0      XVector_0.10.0       Rsamtools_1.22.0    
[34] gridExtra_2.0.0      ggplot2_1.0.1        digest_0.6.8        
[37] stringi_1.0-1        grid_3.2.2           tools_3.2.2         
[40] bitops_1.0-6         magrittr_1.5         RCurl_1.95-4.7      
[43] RSQLite_1.0.0        Formula_1.2-1        cluster_2.0.3       
[46] futile.options_1.0.0 MASS_7.3-45          rpart_4.1-10        
[49] nnet_7.3-11

 

ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by Assa Yeroslaviz1.3k
2
gravatar for Alejandro Reyes
2.0 years ago by
Alejandro Reyes1.5k
Dana-Farber Cancer Institute, Boston, USA
Alejandro Reyes1.5k wrote:
Hi, Sorry for the uninformative error message, could you try to set fitExpToVar="treatment"? Alejandro
ADD COMMENTlink written 2.0 years ago by Alejandro Reyes1.5k
This is a parameter ofthe DEXSeqHTML function!
ADD REPLYlink written 2.0 years ago by Alejandro Reyes1.5k
0
gravatar for Assa Yeroslaviz
2.0 years ago by
Assa Yeroslaviz1.3k
Munich, Germany
Assa Yeroslaviz1.3k wrote:

yes, that did it

thanks

 

ADD COMMENTlink written 2.0 years ago by Assa Yeroslaviz1.3k
0
gravatar for Assa Yeroslaviz
2.0 years ago by
Assa Yeroslaviz1.3k
Munich, Germany
Assa Yeroslaviz1.3k wrote:

Hi Alejandro,

 

now i am getting a new error message

> CR4W0h.CTRL0hdxd = testForDEU( CR4W0h.CTRL0hdxd,  BPPARAM = BPPARAM)
using supplied model matrix
...
using supplied model matrix
Error in .rbind.SummarizedExperiment(args) :
  '...' objects must have the same number of samples


Even though I do have now the same number of samples for my two conditions, I can't understand if that the real problem here:

> CR4W0h.CTRL0hsampleTable
       sampleName treatment replica timepoint   group
CR4Wo1     CR4Wo1     CR4Wo       1        0h CR4Wo0h
CR4Wo2     CR4Wo2     CR4Wo       2        0h CR4Wo0h
CR4Wo3     CR4Wo3     CR4Wo       3        0h CR4Wo0h
CR4Wo4     CR4Wo4     CR4Wo       4        0h CR4Wo0h
C20           C20      ctrl       1        0h  ctrl0h
C22           C22      ctrl       2        0h  ctrl0h
C23           C23      ctrl       3        0h  ctrl0h
C24           C24      ctrl       4        0h  ctrl0h

Any ideas?

 

I hope I don't have to update any other packages.

 

thanks

Assa

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8   
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8  
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] 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
[8] methods   base

other attached packages:
 [1] DEXSeq_1.16.2              DESeq2_1.10.0
 [3] RcppArmadillo_0.6.200.2.0  Rcpp_0.12.2
 [5] SummarizedExperiment_1.0.1 GenomicRanges_1.22.1
 [7] GenomeInfoDb_1.6.1         IRanges_2.4.4
 [9] S4Vectors_0.8.3            Biobase_2.30.0
[11] BiocGenerics_0.16.1        BiocParallel_1.4.0

loaded via a namespace (and not attached):
 [1] genefilter_1.52.0    statmod_1.4.22       locfit_1.5-9.1
 [4] reshape2_1.4.1       splines_3.2.2        lattice_0.20-33
 [7] colorspace_1.2-6     survival_2.38-3      XML_3.98-1.3
[10] foreign_0.8-66       DBI_0.3.1            RColorBrewer_1.1-2
[13] lambda.r_1.1.7       plyr_1.8.3           stringr_1.0.0
[16] zlibbioc_1.16.0      Biostrings_2.38.2    munsell_0.4.2
[19] gtable_0.1.2         futile.logger_1.4.1  hwriter_1.3.2
[22] latticeExtra_0.6-26  geneplotter_1.48.0   biomaRt_2.26.0
[25] AnnotationDbi_1.32.0 proto_0.3-10         acepack_1.3-3.3
[28] xtable_1.8-0         scales_0.3.0         Hmisc_3.17-0
[31] annotate_1.48.0      XVector_0.10.0       Rsamtools_1.22.0
[34] gridExtra_2.0.0      ggplot2_1.0.1        digest_0.6.8
[37] stringi_1.0-1        grid_3.2.2           tools_3.2.2
[40] bitops_1.0-6         magrittr_1.5         RCurl_1.95-4.7
[43] RSQLite_1.0.0        Formula_1.2-1        cluster_2.0.3
[46] futile.options_1.0.0 MASS_7.3-45          rpart_4.1-10
[49] nnet_7.3-11

 

 

 

 

ADD COMMENTlink written 2.0 years ago by Assa Yeroslaviz1.3k
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