Hi, I am using apeglm to do Log fold change shrinkage to help during visualization of data, and after running

`lfcShrink(dds, coef="condition_min_vs_control", type="apeglm")``r

I get the following error:

Warning messages: 1: In nbinomGLM(x = x, Y = YNZ, size = size, weights = weightsNZ, offset = offsetNZ, : the line search routine failed, possibly due to insufficient numeric precision 2: In nbinomGLM(x = x, Y = YNZ, size = size, weights = weightsNZ, offset = offsetNZ, : the line search routine failed, possibly due to insufficient numeric precision 3: In nbinomGLM(x = x, Y = YNZ, size = size, weights = weightsNZ, offset = offsetNZ, : the line search routine failed, possibly due to insufficient numeric precision 4: In nbinomGLM(x = x, Y = YNZ, size = size, weights = weightsNZ, offset = offsetNZ, : the line search routine failed, possibly due to insufficient numeric precision

Any idea of why this is happening, and how to fix it? I ran DESeq2.

Thanks;

sessionInfo( ) R version 4.3.0 (2023-04-21 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
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

time zone: America/New_York tzcode source: internal

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

other attached packages: [1] DESeq2_1.40.2 SummarizedExperiment_1.30.2 Biobase_2.60.0
[4] MatrixGenerics_1.12.3 matrixStats_1.0.0 GenomicRanges_1.52.0
[7] GenomeInfoDb_1.36.1 IRanges_2.34.1 S4Vectors_0.38.1
[10] BiocGenerics_0.46.0

loaded via a namespace (and not attached): [1] utf8_1.2.3 generics_0.1.3 bitops_1.0-7 lattice_0.21-8
[5] magrittr_2.0.3 grid_4.3.0 mvtnorm_1.2-2 plyr_1.8.8
[9] Matrix_1.5-4 BiocManager_1.30.22 fansi_1.0.4 scales_1.2.1
[13] numDeriv_2016.8-1.1 codetools_0.2-19 emdbook_1.3.13 abind_1.4-5
[17] cli_3.6.1 bbmle_1.0.25 rlang_1.1.1 crayon_1.5.2
[21] XVector_0.40.0 munsell_0.5.0 DelayedArray_0.26.7 S4Arrays_1.0.5
[25] tools_4.3.0 parallel_4.3.0 BiocParallel_1.34.2 coda_0.19-4
[29] bdsmatrix_1.3-6 dplyr_1.1.2 colorspace_2.1-0 ggplot2_3.4.3
[33] locfit_1.5-9.8 GenomeInfoDbData_1.2.10 vctrs_0.6.3 R6_2.5.1
[37] lifecycle_1.0.3 zlibbioc_1.46.0 MASS_7.3-58.4 pkgconfig_2.0.3
[41] pillar_1.9.0 gtable_0.3.3 glue_1.6.2 Rcpp_1.0.11
[45] tibble_3.2.1 tidyselect_1.2.0 rstudioapi_0.15.0 apeglm_1.22.1
[49] compiler_4.3.0 RCurl_1.98-1.12 ```

What is your design, sample size?

(Also note this is a warning not an error)

Hi, I experienced this warning as well. When I looked at the output I realized that I had not removed all the transcripts with baseMean=0. Once I removed those records, the function ran without warning. Here is my code for keeping the records with more than 1 count:

starting with the RangedSummarizedExperiment object from tximeta()

keep <- rowSums(data.tximeta@assays@data@listData$counts) > 1

data.tximeta1 <- data.tximeta[keep,]

nrow(data.tximeta1) #should see a large reduction in the number of rows

Hope this helps