Error in BSmooth.tstat - stopifnot(length(group1) + length(group2) >= 3) #106
Comments
|
The error tells you don't have enough samples to calculate a variance, and
this seems expected since you only have 2 groups with 1 sample in each
group.
Best,
Kasper
…On Wed, Jan 26, 2022 at 9:41 AM wangjingwan ***@***.***> wrote:
Hi,
I'm testing the package with two test samples (100,000 methylation loci)
and I've encountered the issue in BSmooth.tstat.
I can upload my test dataset in google drive if you need them for
inspection.
R command
all.tstat <- BSmooth.tstat(all.filtered,
group1 = c("ho_test"),
group2 = c("ho_pa_test"),
estimate.var = "group2",
local.correct = TRUE,
verbose = TRUE)
R error
Error in BSmooth.tstat(all.filtered, group1 = c("ho_test"), group2 = c("ho_pa_test"), : length(group1) + length(group2) >= 3 is not TRUETraceback:
1. BSmooth.tstat(all.filtered, group1 = c("ho_test"), group2 = c("ho_pa_test"),
. estimate.var = "group2", local.correct = TRUE, verbose = TRUE)2. stopifnot(length(group1) + length(group2) >= 3)
R sessionInfo
* sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936
[2] LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936
[4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] bsseq_1.30.0 SummarizedExperiment_1.24.0
[3] Biobase_2.54.0 MatrixGenerics_1.6.0
[5] matrixStats_0.61.0 GenomicRanges_1.46.1
[7] GenomeInfoDb_1.30.0 IRanges_2.28.0
[9] S4Vectors_0.32.3 BiocGenerics_0.40.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 locfit_1.5-9.4
[3] lattice_0.20-45 snow_0.4-4
[5] Rsamtools_2.10.0 Biostrings_2.62.0
[7] gtools_3.9.2 digest_0.6.29
[9] utf8_1.2.2 IRdisplay_1.1
[11] R6_2.5.1 repr_1.1.4
[13] evaluate_0.14 pillar_1.6.5
[15] sparseMatrixStats_1.6.0 zlibbioc_1.40.0
[17] rlang_0.4.12 uuid_1.0-3
[19] data.table_1.14.2 R.oo_1.24.0
[21] R.utils_2.11.0 Matrix_1.4-0
[23] BiocParallel_1.28.3 RCurl_1.98-1.5
[25] munsell_0.5.0 DelayedArray_0.20.0
[27] HDF5Array_1.22.1 compiler_4.1.2
[29] rtracklayer_1.54.0 base64enc_0.1-3
[31] htmltools_0.5.2 GenomeInfoDbData_1.2.7
[33] XML_3.99-0.8 fansi_0.5.0
[35] permute_0.9-5 crayon_1.4.2
[37] R.methodsS3_1.8.1 GenomicAlignments_1.30.0
[39] rhdf5filters_1.6.0 bitops_1.0-7
[41] grid_4.1.2 jsonlite_1.7.2
[43] lifecycle_1.0.1 scales_1.1.1
[45] XVector_0.34.0 limma_3.50.0
[47] DelayedMatrixStats_1.16.0 ellipsis_0.3.2
[49] vctrs_0.3.8 IRkernel_1.3
[51] Rhdf5lib_1.16.0 rjson_0.2.21
[53] restfulr_0.0.13 tools_4.1.2
[55] BSgenome_1.62.0 glue_1.6.0
[57] parallel_4.1.2 fastmap_1.1.0
[59] yaml_2.2.1 colorspace_2.0-2
[61] rhdf5_2.38.0 BiocManager_1.30.16
[63] pbdZMQ_0.3-6 BiocIO_1.4.0
Bioconductor version '3.14'
* 7 packages out-of-date
* 0 packages too new
create a valid installation with
BiocManager::install(c(
"fansi", "glue", "jsonlite", "Rcpp", "RcppArmadillo", "reticulate", "yaml"
), update = TRUE, ask = FALSE)
more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date
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--
Best,
Kasper
|
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So what should I do if I only want to compare one treatment and one control sample? |
|
Hi, R command all.tstat <- BSmooth.tstat(all.filtered,
group1 = c("ho_test","ho_test2"),
group2 = c("ho_pa_test"),
estimate.var = "group2",
local.correct = TRUE,
verbose = TRUE)R error [BSmooth.tstat] preprocessing ... done in 0.0 sec
[BSmooth.tstat] computing stats within groups ... done in 0.0 sec
[BSmooth.tstat] computing stats across groups ...
Error in h(simpleError(msg, call)): error in evaluating the argument 'args' in selecting a method for function 'do.call': need at least two non-NA values to interpolate
Traceback:
1. BSmooth.tstat(all.filtered, group1 = c("ho_test", "ho_test2"),
. group2 = c("ho_pa_test"), estimate.var = "group2", local.correct = TRUE,
. verbose = TRUE)
2. do.call(c, mclapply(clusterIdx, compute.correction, qSd = qSd,
. mc.cores = mc.cores))
3. mclapply(clusterIdx, compute.correction, qSd = qSd, mc.cores = mc.cores)
4. lapply(X, FUN, ...)
5. FUN(X[[i]], ...)
6. approxfun(xx, yy)
7. stop("need at least two non-NA values to interpolate")
8. .handleSimpleError(function (cond)
. .Internal(C_tryCatchHelper(addr, 1L, cond)), "need at least two non-NA values to interpolate",
. base::quote(approxfun(xx, yy)))
9. h(simpleError(msg, call)) |
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Hi,
I'm testing the package with two test samples (100,000 methylation loci) and I've encountered the issue in BSmooth.tstat.
I can upload my test dataset in google drive if you need them for inspection.
Thank you.
R command
R error
R sessionInfo
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