Warnings when using "ashr" in lfcshrinkage for DESeq2
2
0
Entering edit mode
@andrebolerbarros-16788
Last seen 27 days ago
Portugal

Hi everyone,

I'm currently getting some warnings when using lfcshrinkage with "ashr", regarding solve().

Example

Code should be placed in three backticks as shown below

library(zebrafishRNASeq)

data(zfGenes)

dds <- DESeqDataSetFromMatrix(countData = zfGenes,
                              colData = data.frame(group=rep(c("Ctl","Trt"),each=3)),
                              design= ~ group)
dm<-dm[rowSums(counts(dm)) > 0 , ] #remove the genes w/ 0 reads
dds <- DESeq(dds)
res <- results(dds, contrast = c("group", "Trt","Ctl"))
ashr_res<-lfcShrink(dds, contrast = c("group", "Trt","Ctl"),type="ashr")

This leads to the production of the corresponding output:

warning: solve(): system is singular (rcond: 4.77692e-17); attempting approx solution

warning: solve(): system is singular (rcond: 6.21768e-17); attempting approx solution

warning: solve(): system is singular (rcond: 9.89691e-17); attempting approx solution

warning: solve(): system is singular (rcond: 6.62855e-17); attempting approx solution

warning: solve(): system is singular (rcond: 7.63405e-17); attempting approx solution

warning: solve(): system is singular (rcond: 7.66601e-17); attempting approx solution

warning: solve(): system is singular (rcond: 7.91531e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.20337e-17); attempting approx solution

Is there anyone getting the same error?

sessionInfo():

R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7600)

Matrix products: default

locale:
[1] LC_COLLATE=Portuguese_Portugal.1252  LC_CTYPE=Portuguese_Portugal.1252   
[3] LC_MONETARY=Portuguese_Portugal.1252 LC_NUMERIC=C                        
[5] LC_TIME=Portuguese_Portugal.1252    

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

other attached packages:
 [1] zebrafishRNASeq_1.14.0      RUVSeq_1.28.0               edgeR_3.36.0               
 [4] limma_3.50.3                EDASeq_2.28.0               ShortRead_1.52.0           
 [7] GenomicAlignments_1.30.0    Rsamtools_2.10.0            Biostrings_2.62.0          
[10] XVector_0.34.0              BiocParallel_1.28.3         openxlsx_4.2.5             
[13] xlsx_0.6.5                  ggprism_1.0.3               vsn_3.62.0                 
[16] gridExtra_2.3               stringr_1.4.0               readxl_1.4.0               
[19] genefilter_1.76.0           ggplot2_3.3.6               org.Mm.eg.db_3.14.0        
[22] AnnotationDbi_1.56.2        RColorBrewer_1.1-3          pheatmap_1.0.12            
[25] DESeq2_1.34.0               SummarizedExperiment_1.24.0 Biobase_2.54.0             
[28] MatrixGenerics_1.6.0        matrixStats_0.62.0          GenomicRanges_1.46.1       
[31] GenomeInfoDb_1.30.1         IRanges_2.28.0              S4Vectors_0.32.4           
[34] BiocGenerics_0.40.0        

loaded via a namespace (and not attached):
  [1] backports_1.4.1        aroma.light_3.24.0     BiocFileCache_2.2.1   
  [4] splines_4.1.2          inline_0.3.19          digest_0.6.29         
  [7] invgamma_1.1           htmltools_0.5.2        SQUAREM_2021.1        
 [10] fansi_1.0.3            magrittr_2.0.3         memoise_2.0.1         
 [13] annotate_1.72.0        RcppParallel_5.1.5     R.utils_2.11.0        
 [16] prettyunits_1.1.1      jpeg_0.1-9             colorspace_2.0-3      
 [19] rappdirs_0.3.3         blob_1.2.3             xfun_0.31             
 [22] dplyr_1.0.9            callr_3.7.0            crayon_1.5.1          
 [25] RCurl_1.98-1.6         survival_3.3-1         glue_1.6.2            
 [28] gtable_0.3.0           zlibbioc_1.40.0        DelayedArray_0.20.0   
 [31] car_3.0-13             pkgbuild_1.3.1         rstan_2.21.5          
 [34] abind_1.4-5            scales_1.2.0           DBI_1.1.2             
 [37] rstatix_0.7.0          Rcpp_1.0.8.3           progress_1.2.2        
 [40] xtable_1.8-4           bit_4.0.4              preprocessCore_1.56.0 
 [43] StanHeaders_2.21.0-7   truncnorm_1.0-8        httr_1.4.3            
 [46] modeltools_0.2-23      ellipsis_0.3.2         pkgconfig_2.0.3       
 [49] loo_2.5.1              XML_3.99-0.9           rJava_1.0-6           
 [52] R.methodsS3_1.8.1      flexmix_2.3-17         farver_2.1.0          
 [55] dbplyr_2.1.1           nnet_7.3-17            locfit_1.5-9.5        
 [58] utf8_1.2.2             tidyselect_1.1.2       labeling_0.4.2        
 [61] rlang_1.0.2            munsell_0.5.0          cellranger_1.1.0      
 [64] tools_4.1.2            cachem_1.0.6           cli_3.2.0             
 [67] generics_0.1.2         RSQLite_2.2.14         broom_0.8.0           
 [70] evaluate_0.15          fastmap_1.1.0          yaml_2.3.5            
 [73] processx_3.5.3         knitr_1.39             bit64_4.0.5           
 [76] zip_2.2.0              purrr_0.3.4            KEGGREST_1.34.0       
 [79] R.oo_1.24.0            xml2_1.3.3             biomaRt_2.50.3        
 [82] compiler_4.1.2         rstudioapi_0.13        filelock_1.0.2        
 [85] curl_4.3.2             png_0.1-7              affyio_1.64.0         
 [88] ggsignif_0.6.3         tibble_3.1.6           geneplotter_1.72.0    
 [91] stringi_1.7.6          ps_1.7.0               GenomicFeatures_1.46.5
 [94] lattice_0.20-45        Matrix_1.4-1           vctrs_0.4.1           
 [97] pillar_1.7.0           lifecycle_1.0.1        BiocManager_1.30.17   
[100] cowplot_1.1.1          bitops_1.0-7           irlba_2.3.5           
[103] rtracklayer_1.54.0     BiocIO_1.4.0           R6_2.5.1              
[106] latticeExtra_0.6-29    affy_1.72.0            hwriter_1.3.2.1       
[109] codetools_0.2-18       MASS_7.3-57            assertthat_0.2.1      
[112] xlsxjars_0.6.1         rjson_0.2.21           withr_2.5.0           
[115] GenomeInfoDbData_1.2.7 hms_1.1.1              parallel_4.1.2        
[118] grid_4.1.2             tidyr_1.2.0            rmarkdown_2.14        
[121] carData_3.0-5          ashr_2.2-54            ggpubr_0.4.0          
[124] mixsqp_0.3-43          lubridate_1.8.0        restfulr_0.0.13

Thanks in advance!

RNASeq DESeq2 • 327 views
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2
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ATpoint ★ 1.3k
@atpoint-13662
Last seen 14 hours ago
Germany

The error comes from the mixsqp package, see https://github.com/stephens999/ashr/issues/131. Upgrading the package to the most recent 0.3.47 via remotes::install_github("stephenslab/mixsqp") solved the issue for me. If you are on Windows you probably need to have both Rtools and the pkgbuild installed as the package requires some compilation when pulling directly via GitHub.

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0
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Upgrading the package solved the issue, thanks!

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1
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@mikelove
Last seen 1 hour ago
United States

Note sure why it's having difficulty converging.

You could use apeglm?

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0
Entering edit mode

Hi Michael,

I'm using the "contrast" parameter, so I cannot use apeglm with that, as far as I know. The "coef" will not allow me to do every comparison I need.

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0
Entering edit mode

Sorry, I haven't seen this. Maybe try filtering low count genes?

keep <- rowSums(counts(dds) >= 10) >= X
dds <- dds[keep,]
# then run DESeq
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0
Entering edit mode

Thanks for the suggestion.

I ran the following filtering criteria:

keep <- rowSums(counts(dds) >= 10) >= 5
dds <- dds[keep,]

It gave the following errors:

warning: solve(): system is singular (rcond: 1.54281e-17); attempting approx solution

warning: solve(): system is singular (rcond: 2.06738e-17); attempting approx solution

warning: solve(): system is singular (rcond: 5.18223e-17); attempting approx solution

warning: solve(): system is singular (rcond: 5.51318e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.45586e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.01227e-16); attempting approx solution
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