Question: DESeqDataSetFromMatrix NA error while there is no NA in the data
gravatar for lucie.laplane
12 weeks ago by
lucie.laplane0 wrote:

Hi, When applying DESeqDataSetFromMatrix() I get this error: Error in DESeqDataSet(se, design = design, ignoreRank) : NA values are not allowed in the count matrix I checked in my counts file, there is not NA. So there must be something wrong in the importation of the data. Here is my code:

# importing the read counts
base <- as.character("./");
counts <- base::file.path(base, "Counts.csv");
counts <- utils::read.table(file = counts, header = TRUE, sep = ";");
counts <- data.frame(counts[,-1], row.names=counts[,1]);

# Creating the metadata
condition <- c("PreT","PreT","PreT","PreT","PreT","PreT","C6D28","C6D28","C6D28","C6D28","C6D28");
batch <- c("PD7154", "PD7155", "PD7153", "PD7151", "PD7156", "PD7157", "PD7155", "PD7153", "PD7151", "PD7156", "PD7157");
metadata <- data.frame(condition, batch);
rownames(metadata) <- c("PD7154", "PD7155", "PD7153", "PD7151_C1D1", "PD7156_C1D1", "PD7157_C1D1", "PD7155_C6D28", "PD7153_C6D28", "PD7151_C6D28", "PD7156_C6D28", "PD7157_C6D28");

# Testing that metadata fits with the counts 
all(rownames(metadata) == colnames(counts));

# Applying DESeqDataSetFromMatrix function
dds <- DESeqDataSetFromMatrix(
  countData = counts,
  colData = metadata,
  design = ~ batch + condition

Bellow are my session info. Thanks for your help.

sessionInfo() R version 3.5.2 (2018-12-20) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.3

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale: [1] C

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

other attached packages: [1] EnhancedVolcano1.0.1 ggrepel0.8.0 magrittr1.5
[4] limma
3.38.3 biomaRt2.38.0 pheatmap1.0.12
[7] RColorBrewer1.1-2 DESeq21.22.2 SummarizedExperiment1.12.0 [10] DelayedArray0.8.0 BiocParallel1.16.6 matrixStats0.54.0
[13] Biobase2.42.0 GenomicRanges1.34.0 GenomeInfoDb1.18.2
[16] IRanges
2.16.0 S4Vectors0.20.1 BiocGenerics0.28.0
[19] ggfortify0.4.5 broom0.5.1 forcats0.4.0
[22] stringr
1.4.0 purrr0.3.0 tidyr0.8.2
[25] tibble2.1.1 ggplot23.1.0 tidyverse1.2.1
[28] dplyr DT0.5 readr1.3.1

loaded via a namespace (and not attached): [1] nlme3.1-137 bitops1.0-6 bit640.9-7
[4] lubridate
1.7.4 progress1.2.0 httr1.4.0
[7] tools3.5.2 backports1.1.3 R62.4.0
[10] rpart
4.1-13 DBI1.0.0 Hmisc4.2-0
[13] lazyeval0.2.1 colorspace1.4-0 nnet7.3-12
[16] withr
2.1.2 prettyunits1.0.2 tidyselect0.2.5
[19] gridExtra2.3 bit1.1-14 compiler3.5.2
[22] cli
1.1.0 rvest0.3.2 htmlTable1.13.1
[25] xml21.2.0 scales1.0.0 checkmate1.9.1
[28] genefilter
1.64.0 digest0.6.18 foreign0.8-71
[31] XVector0.22.0 base64enc0.1-3 pkgconfig2.0.2
[34] htmltools
0.3.6 htmlwidgets1.3 rlang0.3.1
[37] readxl1.3.0 RSQLite2.1.1 rstudioapi0.9.0
[40] generics
0.0.2 jsonlite1.6 acepack1.4.1
[43] RCurl1.95-4.11 GenomeInfoDbData1.2.0 Formula1.2-3
[46] Matrix
1.2-15 Rcpp1.0.1 munsell0.5.0
[49] yaml2.2.0 stringi1.3.1 zlibbioc1.28.0
[52] plyr
1.8.4 blob1.1.1 grid3.5.2
[55] crayon1.3.4 lattice0.20-38 haven2.1.0
[58] annotate
1.60.0 hms0.4.2 locfit1.5-9.1
[61] knitr1.21 pillar1.3.1 geneplotter1.60.0
[64] XML
3.98-1.17 glue1.3.0 latticeExtra0.6-28
[67] data.table1.12.0 modelr0.1.4 cellranger1.1.0
[70] gtable
0.2.0 assertthat0.2.1 xfun0.5
[73] xtable1.8-3 survival2.43-3 memoise1.1.0
[76] AnnotationDbi
1.44.0 cluster_2.0.7-1

deseq2 • 69 views
ADD COMMENTlink modified 12 weeks ago by Michael Love24k • written 12 weeks ago by lucie.laplane0
Answer: DESeqDataSetFromMatrix NA error while there is no NA in the data
gravatar for Michael Love
12 weeks ago by
Michael Love24k
United States
Michael Love24k wrote:

You can debug yourself a bit: take a look at counts and find where the NAs are.

ADD COMMENTlink written 12 weeks ago by Michael Love24k
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