collapseReplicates dimension error
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Entering edit mode
Léa • 0
@ef49a400
Last seen 25 days ago
France

Hello,

I am trying to re-analyze public data from this deposit on DESeq2: https://github.com/Ellen1101/OA-subtype/tree/master

The counts matrix is available in the "cartilage.count.201905113.zip" file, and metadata is stored in the "cart_ann_20190513.txt" file. I used the following code to load the data, and at the very first step when I try to collapse technical replicates I get an error of dimension, like one matrix is transposed the wrong way.

Error in [[<-(`tmp`, name, value = new("DESeqDataSet", design = ~Group, : 58684 elements in value to replace 232 elements

What can I do to proceed?

Here is the code :

counts = read.table(file = "Yuan2020/cartilage.count.201905113.txt",
                    header = TRUE)

counts.matrix = counts %>% 
  select(c(7:238))
rownames(counts.matrix)= counts$Geneid


metadata = read.table(file = "Yuan2020/cart_ann_20190513.txt", 
                      header = TRUE, 
                      na.strings = "N",
                      stringsAsFactors = TRUE
                      ) %>% 
  mutate(runID = libID_cart02) %>% 
  mutate(sampleID = as.factor(sampleID)) %>% 
  select(-c("libID_cart02")) #simplify name

length(levels(metadata$sampleID)) # 217 samples for 232 runs
table(metadata$sampleID) # some samples have been run twice
table(metadata[,"runID"]) #Ok this is unique


### Load to DESeq
ddsFullCountTable <- DESeqDataSetFromMatrix(countData = counts.matrix, 
                                            colData   = metadata, 
                                            design    = ~ Group)
ddsFullCountTable$
# Collapse replicates
ddsCollapsed <- collapseReplicates(ddsFullCountTable, 
                                   groupby = metadata$sampleID, run = metadata$runID)
sessionInfo()

And here is the session info:

R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                           LC_TIME=English_United States.utf8    

time zone: Europe/Paris
tzcode source: internal

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

other attached packages:
 [1] DESeq2_1.40.2               tidyselect_1.2.1            dplyr_1.1.4                 SingleCellExperiment_1.24.0 SummarizedExperiment_1.32.0
 [6] Biobase_2.62.0              GenomicRanges_1.54.1        GenomeInfoDb_1.38.7         IRanges_2.36.0              S4Vectors_0.40.2           
[11] BiocGenerics_0.48.1         MatrixGenerics_1.14.0       matrixStats_1.2.0          

loaded via a namespace (and not attached):
 [1] gtable_0.3.4            xfun_0.42               ggplot2_3.5.0           htmlwidgets_1.6.4       rstatix_0.7.2           lattice_0.22-5         
 [7] vctrs_0.6.5             tools_4.3.2             bitops_1.0-7            generics_0.1.3          parallel_4.3.2          tibble_3.2.1           
[13] fansi_1.0.6             pkgconfig_2.0.3         Matrix_1.6-5            data.table_1.15.2       lifecycle_1.0.4         GenomeInfoDbData_1.2.11
[19] compiler_4.3.2          munsell_0.5.0           codetools_0.2-19        carData_3.0-5           htmltools_0.5.7         RCurl_1.98-1.14        
[25] yaml_2.3.8              lazyeval_0.2.2          plotly_4.10.4           pillar_1.9.0            car_3.1-2               ggpubr_0.6.0           
[31] crayon_1.5.2            tidyr_1.3.1             BiocParallel_1.36.0     DelayedArray_0.28.0     sessioninfo_1.2.2       abind_1.4-5            
[37] locfit_1.5-9.9          digest_0.6.35           purrr_1.0.2             fastmap_1.1.1           grid_4.3.2              SparseArray_1.2.4      
[43] colorspace_2.1-0        cli_3.6.2               magrittr_2.0.3          S4Arrays_1.2.1          utf8_1.2.4              broom_1.0.5            
[49] withr_3.0.0             scales_1.3.0            backports_1.4.1         rmarkdown_2.26          XVector_0.42.0          httr_1.4.7             
[55] ggsignif_0.6.4          evaluate_0.23           knitr_1.45              viridisLite_0.4.2       rlang_1.1.3             Rcpp_1.0.12            
[61] glue_1.7.0              pROC_1.18.5             pkgload_1.3.4           rstudioapi_0.15.0       jsonlite_1.8.8          R6_2.5.1               
[67] plyr_1.8.9              zlibbioc_1.48.0        

Thanks !

DESeq2 Dese • 150 views
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Entering edit mode
@mikelove
Last seen 18 hours ago
United States

Try skipping specifying run.

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