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I want run deseq2 from tximport data. for sample dataset I can able to create deseq2 matrix file but for own data getting error i have kept same row(15) and column(15) name in condition and count data still getting error i have seen many already available question mentioned to update the versions after updating the version getting same error
please help
Thank you
library(DESeq2)
library(tximport)
dir <- "counting"
samples = read.table('Sample.txt', sep="\t", header = T, row.names = 1)
tx2gene = read.table('Transcript_gene_id.txt', sep = '\t', header = T)
files <- file.path(dir, "", samples$Path, "quant.sf")
names(files) <- row.names(samples)
all(file.exists(files))
txi = tximport(files = files, type = 'salmon', tx2gene = tx2gene)
rownames(samples ) <- colnames(txi$counts)
all(colnames(txi$counts) %in% rownames(samples))
all(colnames(txi$counts) == rownames(samples))
dds <- DESeqDataSetFromMatrix(txi, samples, ~Type1)
Error in validObject(.Object) :
invalid class SummarizedExperiment object:
nb of cols in assay(1) must equal nb of rows in colData(15)
sessionInfo( )
R version 4.2.0 (2022-04-22)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 22.04.4 LTS
Matrix products: default
BLAS/LAPACK: /media/anaconda3/lib/libopenblasp-r0.3.21.so
locale:
[1] LC_CTYPE=en_IN.UTF-8 LC_NUMERIC=C LC_TIME=en_IN.UTF-8 LC_COLLATE=en_IN.UTF-8
[5] LC_MONETARY=en_IN.UTF-8 LC_MESSAGES=en_IN.UTF-8 LC_PAPER=en_IN.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] tximport_1.26.1 DESeq2_1.38.3 SummarizedExperiment_1.28.0 Biobase_2.58.0
[5] MatrixGenerics_1.10.0 matrixStats_1.2.0 GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
[9] IRanges_2.32.0 S4Vectors_0.36.2 BiocGenerics_0.44.0
loaded via a namespace (and not attached):
[1] KEGGREST_1.38.0 locfit_1.5-9.9 tidyselect_1.2.1 lattice_0.22-5 generics_0.1.3
[6] colorspace_2.1-0 vctrs_0.6.5 utf8_1.2.4 blob_1.2.4 XML_3.99-0.14
[11] rlang_1.1.3 pillar_1.9.0 glue_1.7.0 DBI_1.2.2 BiocParallel_1.32.6
[16] bit64_4.0.5 RColorBrewer_1.1-3 GenomeInfoDbData_1.2.9 lifecycle_1.0.4 zlibbioc_1.44.0
[21] Biostrings_2.66.0 munsell_0.5.0 gtable_0.3.4 codetools_0.2-19 memoise_2.0.1
[26] geneplotter_1.76.0 fastmap_1.1.1 parallel_4.2.0 fansi_1.0.6 AnnotationDbi_1.60.2
[31] Rcpp_1.0.12 xtable_1.8-4 scales_1.3.0 BiocManager_1.30.22 cachem_1.0.8
[36] DelayedArray_0.24.0 jsonlite_1.8.8 annotate_1.76.0 XVector_0.38.0 bit_4.0.5
[41] ggplot2_3.5.0 png_0.1-8 dplyr_1.1.4 grid_4.2.0 cli_3.6.2
[46] tools_4.2.0 bitops_1.0-7 magrittr_2.0.3 RCurl_1.98-1.14 RSQLite_2.3.5
[51] tibble_3.2.1 pkgconfig_2.0.3 crayon_1.5.2 Matrix_1.6-5 httr_1.4.7
[56] rstudioapi_0.15.0 R6_2.5.1 compiler_4.2.0
