DESeq2 Error: Error in if (assays_nrow != rowData_nrow) { : argument is of length zero
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929072397 • 0
@929072397-15330
Last seen 6.0 years ago

Hi, everyone,

I'm running this line in DESeq2 1.18.1

dds1<-DESeqDataSetFromMatrix(countData = countdata1,colData = coldata1,design= ~ day+treatment)

but a error happened:

Error in if (assays_nrow != rowData_nrow) { : argument is of length zero.

Why this happen? I have run this line many times and it is OK previously. 

This is my countdata1 and coldata1:

head(coldata1)
      day  treatment       specific
M1D0    0 Pulse_AgNP   0_Pulse_AgNP
M1D1    1 Pulse_AgNP   1_Pulse_AgNP
M1D3    3 Pulse_AgNP   3_Pulse_AgNP
M1D7    7 Pulse_AgNP   7_Pulse_AgNP
M1D14  14 Pulse_AgNP  14_Pulse_AgNP
M1D28  28 Pulse_AgNP  28_Pulse_AgNP


head(countdata1)
          M1D0    M1D1    M1D3   M1D7  M1D14  M1D28  M1D98 M1D126 M1D203 M1D273 M1D330 M1D364   M2D0  M2D1   M2D3
OTU_6   278673   17123    1004   2095 626380  77239      0      0    397 163044 509196  68142   7962  5299   5280
OTU_19    1203       0       0      0      0 937508  34179      0  44977 355505 387525 257265   4993  1342   1738
OTU_2    62826       0       0    274 100277 246938 248305   5420 181724  95374  46374 391341 270635  3524   3470
OTU_1     3161 1534582 1812810  34913      0      0      0      0      0      0      0      0   5580 83355 100648
OTU_3  1112313   19966       0 557619 142265  89957   2742      0   3740  64226 140615 109204   9936  3505  62165
OTU_4    72835    5643       0      0      0  37732 100159  47225 214901  70906   9343  66331 101244 49405 255815
         M2D7  M2D14  M2D28  M2D98 M2D126 M2D203 M2D273 M2D330 M2D364   M4D0   M4D1   M4D3   M4D7  M4D14  M4D28 M4D98
OTU_6     917  11980  71046      0      0      0 238108  94303 324842 991990 125947 167798 377852 787716 476976     0
OTU_19 395554  75254  81272  42580    907 224528 104372 739969 250072      0      0      0      0      0    798     0
OTU_2   18089  19281 118060 348372  19282 200200  46904 334915 181795   4418      0    336      0  19017  67724 56881
OTU_1       0      0    197      0      0      0    304      0      0      0  27745 379477   3329      0      0     0
OTU_3  412329 510225 307706  53054   2351      0 119184 105990  18294      0      0    713      0  45043 294026  1572
OTU_4  241904  70083  98436  44923 113886   3690 279220  24777 288650 196250  35663  56211 141811 116604   3144     0

And the sessioninfo:

sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] DESeq2_1.18.1              SummarizedExperiment_1.8.1 DelayedArray_0.4.1         matrixStats_0.53.1        
 [5] Biobase_2.38.0             GenomicRanges_1.30.0       GenomeInfoDb_1.14.0        IRanges_2.12.0            
 [9] S4Vectors_0.16.0           BiocGenerics_0.24.0       

loaded via a namespace (and not attached):
 [1] genefilter_1.60.0      locfit_1.5-9.1         splines_3.4.4          lattice_0.20-35        colorspace_1.3-2      
 [6] htmltools_0.3.6        yaml_2.1.18            base64enc_0.1-3        blob_1.1.0             survival_2.41-3       
[11] XML_3.98-1.10          rlang_0.2.0            pillar_1.2.1           DBI_0.8                foreign_0.8-69        
[16] BiocParallel_1.12.0    bit64_0.9-7            RColorBrewer_1.1-2     GenomeInfoDbData_1.0.0 plyr_1.8.4            
[21] stringr_1.3.0          zlibbioc_1.24.0        munsell_0.4.3          gtable_0.2.0           htmlwidgets_1.0       
[26] memoise_1.1.0          latticeExtra_0.6-28    knitr_1.20             geneplotter_1.56.0     AnnotationDbi_1.40.0  
[31] htmlTable_1.11.2       Rcpp_0.12.16           acepack_1.4.1          xtable_1.8-2           scales_0.5.0          
[36] backports_1.1.2        checkmate_1.8.5        Hmisc_4.1-1            annotate_1.56.1        XVector_0.18.0        
[41] bit_1.1-12             gridExtra_2.3          ggplot2_2.2.1          digest_0.6.15          stringi_1.1.7         
[46] grid_3.4.4             tools_3.4.4            bitops_1.0-6           magrittr_1.5           RSQLite_2.0           
[51] lazyeval_0.2.1         RCurl_1.95-4.10        tibble_1.4.2           Formula_1.2-2          cluster_2.0.6         
[56] Matrix_1.2-12          data.table_1.10.4-3    rstudioapi_0.7         rpart_4.1-13           nnet_7.3-12           
[61] compiler_3.4.4 

 

Thank for any help!

Oliver

 

deseq2 • 890 views
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0
Entering edit mode
929072397 • 0
@929072397-15330
Last seen 6.0 years ago

Just for notice, the error disappeared when I re-open the Rstudio...... I did nothing to the input data.

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