Question: DESeqDataSetFromTximport gives <Object with null pointer>
0
gravatar for sweissmann
27 days ago by
sweissmann0
sweissmann0 wrote:

Hi, I have been using DESeq2 in RStudio for a long time. I started having problems after updating to R 3.6.0. When using the standard function DESeqDataSetFromTximport like so:

' ' '

dds <- DESeq2::DESeqDataSetFromTximport( txi, design, ~treatment+genotype+timepoint) using counts and average transcript lengths from tximport Warning message: In DESeqDataSet(se, design = design, ignoreRank) : some variables in design formula are characters, converting to factors

Where: - txi is a Tximport object: ' ' '

str(txi) List of 4 $ abundance : num [1:35764, 1:150] 0 3.03 14.25 0 0 ... ..- attr(, "dimnames")=List of 2 .. ..$ : chr [1:35764] "Bradi0012s00100" "Bradi0012s00201" "Bradi0014s00100" "Bradi0135s00100" ... .. ..$ : chr [1:150] "A1" "D1" "A3" "B3" ... $ counts : num [1:35764, 1:150] 0 23 228 0 0 ... ..- attr(, "dimnames")=List of 2 .. ..$ : chr [1:35764] "Bradi0012s00100" "Bradi0012s00201" "Bradi0014s00100" "Bradi0135s00100" ... .. ..$ : chr [1:150] "A1" "D1" "A3" "B3" ... $ length : num [1:35764, 1:150] 1481 1340 2820 926 791 ... ..- attr(, "dimnames")=List of 2 .. ..$ : chr [1:35764] "Bradi0012s00100" "Bradi0012s00201" "Bradi0014s00100" "Bradi0135s00100" ... .. ..$ : chr [1:150] "A1" "D1" "A3" "B3" ... $ countsFromAbundance: chr "no" - attr(, "class")= chr "S4" ' ' '

  • design is a metadata table: genotype timepoint treatment libType A1 Bd21 1 22.5 single-end D1 Bd21 1 22.5 single-end A3 Bd21 1 90 single-end B3 Bd21 1 90 single-end C3 Bd21 1 90 single-end D3 Bd21 1 90 single-end

But: the result object appears as "Object with null pointer"

' ' '

str(dds) Formal class 'DESeqDataSet' [package "DESeq2"] with 8 slots ..@ design :Class 'formula' language ~treatment + genotype + timepoint .. .. ..- attr(, ".Environment")=<environment: r_globalenv=""> ..@ dispersionFunction:function ()
..@ rowRanges :Formal class 'CompressedGRangesList' [package "GenomicRanges"] with 5 slots .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 7 slots .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","
": .. .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. .. ..@ iscircular: logi(0) .. .. .. .. .. .. ..@ genome : chr(0) .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. ..@ metadata : list() .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. ..@ rownames : NULL .. .. .. .. ..@ nrows : int 35764 .. .. .. .. ..@ listData : Named list() .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. .. ..@ listData :List of 2 .. .. .. .. .. .. .. ..$ type : chr(0) .. .. .. .. .. .. .. ..$ description: chr(0) .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. ..@ metadata : list() .. .. ..@ elementType : chr "GRanges" .. .. ..@ metadata : list() .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. ..@ end : int [1:35764] 0 0 0 0 0 0 0 0 0 0 ... .. .. .. .. ..@ NAMES : chr [1:35764] "Bradi0012s00100" "Bradi0012s00201" "Bradi0014s00100" "Bradi0135s00100" ... .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. ..@ metadata : list() ..@ colData :Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. ..@ rownames : chr [1:150] "A1" "D1" "A3" "B3" ... .. .. ..@ nrows : int 150 .. .. ..@ listData :List of 4 .. .. .. ..$ genotype : Factor w/ 2 levels "Bd21","Bd3.1": 1 1 1 1 1 1 2 2 2 2 ... .. .. .. ..$ timepoint: Factor w/ 10 levels "1","2","3","4",..: 1 1 1 1 1 1 1 1 1 1 ... .. .. .. ..$ treatment: Factor w/ 3 levels "22.5","90","Recovery": 1 1 2 2 2 2 1 1 1 2 ... .. .. .. ..$ libType : chr [1:150] "single-end" "single-end" "single-end" "single-end" ... .. .. ..@ elementType : chr "ANY" .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. ..@ rownames : NULL .. .. .. .. ..@ nrows : int 4 .. .. .. .. ..@ listData :List of 2 .. .. .. .. .. ..$ type : chr [1:4] "input" "input" "input" "input" .. .. .. .. .. ..$ description: chr [1:4] "" "" "" "" .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. ..@ metadata : list() .. .. ..@ metadata : list() ..@ assays :Reference class 'ShallowSimpleListAssays' [package "SummarizedExperiment"] with 1 field .. ..$ data: NULL .. ..and 14 methods. ..@ NAMES : NULL ..@ elementMetadata :Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. ..@ rownames : NULL .. .. ..@ nrows : int 35764 .. .. ..@ listData : Named list() .. .. ..@ elementType : chr "ANY" .. .. ..@ elementMetadata: NULL .. .. ..@ metadata : list() ..@ metadata :List of 1 .. ..$ version:Classes 'packageversion', 'numeric_version' hidden list of 1 .. .. ..$ : int [1:3] 1 24 0 ' ' ' Am I doing anything wrong? I use the same script every time. Thanks! Sarit

This is the session info: ' ' '

sessionInfo() R version 3.6.0 (2019-04-26) Platform: x8664-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17134) Matrix products: default Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding locale: [1] LCCOLLATE=EnglishUnited States.1252 LCCTYPE=EnglishUnited States.1252
[3] LC
MONETARY=EnglishUnited States.1252 LCNUMERIC=C
[5] LCTIME=EnglishUnited States.1252
attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] WGCNA1.68 fastcluster1.1.25 dynamicTreeCut1.63-1
[4] DiffBind
2.12.0 DESeq21.24.0 SummarizedExperiment1.14.0 [7] DelayedArray0.10.0 BiocParallel1.17.18 matrixStats0.54.0
[10] Biobase
2.44.0 GenomicRanges1.36.0 GenomeInfoDb1.20.0
[13] IRanges2.18.1 S4Vectors0.22.0 BiocGenerics0.30.0
[16] tximport
1.12.1 ggplot23.2.0 readr1.3.1
[19] stringr1.4.0 tibble2.1.3 forcats0.4.0
[22] purrr
0.3.2 dplyr0.8.1 tidyr0.8.3
[25] BiocManager1.30.4
loaded via a namespace (and not attached): [1] amap
0.8-17 colorspace1.4-1 rjson0.2.20
[4] hwriter1.3.2 htmlTable1.13.1 XVector0.24.0
[7] base64enc
0.1-3 rstudioapi0.10 ggrepel0.8.1
[10] bit640.9-7 mvtnorm1.0-10 AnnotationDbi1.46.0
[13] codetools
0.2-16 splines3.6.0 doParallel1.0.14
[16] robustbase0.93-5 impute1.58.0 geneplotter1.62.0
[19] knitr
1.23 Formula1.2-3 Rsamtools2.0.0
[22] annotate1.62.0 cluster2.0.9 GO.db3.8.2
[25] pheatmap
1.0.12 graph1.62.0 rrcov1.4-7
[28] compiler3.6.0 httr1.4.0 GOstats2.50.0
[31] backports
1.1.4 assertthat0.2.1 Matrix1.2-17
[34] lazyeval0.2.2 limma3.40.2 acepack1.4.1
[37] htmltools
0.3.6 prettyunits1.0.2 tools3.6.0
[40] gtable0.3.0 glue1.3.1 GenomeInfoDbData1.2.1
[43] Category
2.50.0 systemPipeR1.18.1 batchtools0.9.11
[46] rappdirs0.3.1 ShortRead1.42.0 Rcpp1.0.1
[49] Biostrings
2.52.0 preprocessCore1.46.0 gdata2.18.0
[52] rtracklayer1.44.0 iterators1.0.10 xfun0.7
[55] gtools
3.8.1 XML3.98-1.20 DEoptimR1.0-8
[58] edgeR3.26.4 MASS7.3-51.4 zlibbioc1.30.0
[61] scales
1.0.0 BSgenome1.52.0 VariantAnnotation1.30.1 [64] hms0.4.2 RBGL1.60.0 RColorBrewer1.1-2
[67] yaml
2.2.0 memoise1.1.0 gridExtra2.3
[70] biomaRt2.40.0 rpart4.1-15 latticeExtra0.6-28
[73] stringi
1.4.3 RSQLite2.1.1 genefilter1.66.0
[76] pcaPP1.9-73 foreach1.4.4 checkmate1.9.3
[79] GenomicFeatures
1.36.1 caTools1.17.1.2 rlang0.3.4
[82] pkgconfig2.0.2 bitops1.0-6 lattice0.20-38
[85] GenomicAlignments
1.20.0 htmlwidgets1.3 robust0.4-18
[88] bit1.1-14 tidyselect0.2.5 GSEABase1.46.0
[91] AnnotationForge
1.26.0 magrittr1.5 R62.4.0
[94] fit.models0.5-14 gplots3.0.1.1 Hmisc4.2-0
[97] base64url
1.4 DBI1.0.0 pillar1.4.1
[100] foreign0.8-71 withr2.1.2 survival2.44-1.1
[103] RCurl
1.95-4.12 nnet7.3-12 crayon1.3.4
[106] KernSmooth2.23-15 progress1.2.2 locfit1.5-9.1
[109] grid
3.6.0 data.table1.12.2 blob1.1.1
[112] Rgraphviz2.28.0 digest0.6.19 xtable1.8-4
[115] brew
1.0-6 munsell_0.5.0

' ' '

deseq2 software error • 65 views
ADD COMMENTlink modified 27 days ago by Michael Love24k • written 27 days ago by sweissmann0
Answer: DESeqDataSetFromTximport gives <Object with null pointer>
0
gravatar for Michael Love
27 days ago by
Michael Love24k
United States
Michael Love24k wrote:

Updated answer:

https://support.bioconductor.org/p/122184/

ADD COMMENTlink modified 24 days ago • written 27 days ago by Michael Love24k

Great. thanks very much! If It gives me problems with RStudio, I'll just switch to Unix...

ADD REPLYlink written 22 days ago by sweissmann0
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 16.09
Traffic: 288 users visited in the last hour