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I am trying to analyse a 2D-TPP experiment using the TPP2D package. The important thing is that the experiment is fully replicated, so each drug concentration was measured twice (n = 2) at 10 different temperatures. In total, 10x TMT10plex experiments (mixture) were used. The config table looks like:
> tt
# A tibble: 20 × 14
Compound Experiment Temperature `126` `127N` `127C` `128N` `128C` `129N` `129C` `130N` `130C` `131N`
<chr> <chr> <dbl> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 drug rep1_red 41.9 5 1 0.143 0.02 0 - - - - -
2 drug rep1_red 43.6 - - - - - 5 1 0.143 0.02 0
3 drug rep1_orange 45.7 5 1 0.143 0.02 0 - - - - -
4 drug rep1_orange 48.7 - - - - - 5 1 0.143 0.02 0
5 drug rep1_yellow 51.5 5 1 0.143 0.02 0 - - - - -
6 drug rep1_yellow 54.2 - - - - - 5 1 0.143 0.02 0
7 drug rep1_green 57 5 1 0.143 0.02 0 - - - - -
8 drug rep1_green 59.9 - - - - - 5 1 0.143 0.02 0
9 drug rep1_blue 62.1 5 1 0.143 0.02 0 - - - - -
10 drug rep1_blue 64 - - - - - 5 1 0.143 0.02 0
11 drug rep2_red 41.9 5 1 0.143 0.02 0 - - - - -
12 drug rep2_red 43.6 - - - - - 5 1 0.143 0.02 0
13 drug rep2_orange 45.7 5 1 0.143 0.02 0 - - - - -
14 drug rep2_orange 48.7 - - - - - 5 1 0.143 0.02 0
15 drug rep2_yellow 51.5 5 1 0.143 0.02 0 - - - - -
16 drug rep2_yellow 54.2 - - - - - 5 1 0.143 0.02 0
17 drug rep2_green 57 5 1 0.143 0.02 0 - - - - -
18 drug rep2_green 59.9 - - - - - 5 1 0.143 0.02 0
19 drug rep2_blue 62.1 5 1 0.143 0.02 0 - - - - -
20 drug rep2_blue 64 - - - - - 5 1 0.143 0.02 0
# 1 more variable: RefCol <chr>
The function call is:
## import both replicates (10 blocks)
import_df <- import2dDataset(configTable = tt,
data = ll,
idVar = "ProteinID",
intensityStr = "INT_",
fcStr = "rel_fc_",
nonZeroCols = "Total Spectral Count",
geneNameVar = "Entry Name",
addCol = "Gene",
qualColName = "Total Peptides",
naStrs = c("NA")
)
The computation runs far longer than normal (several minutes) and in the end returns no value. Just using the rep1 or rep2 related parts work without any problems. Does anyone know how so solve this issue?
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocParallel_1.28.3 TPP2D_1.10.0 dplyr_1.1.2 tibble_3.2.1 readr_2.1.4
loaded via a namespace (and not attached):
[1] zip_2.3.0 Rcpp_1.0.10 pillar_1.9.0 compiler_4.1.2 bitops_1.0-7
[6] iterators_1.0.14 tools_4.1.2 pkgload_1.3.2 bit_4.0.5 lifecycle_1.0.3
[11] gtable_0.3.3 lattice_0.21-8 pkgconfig_2.0.3 rlang_1.1.1 openxlsx_4.2.5.2
[16] foreach_1.5.2 cli_3.6.1 rstudioapi_0.14 parallel_4.1.2 withr_2.5.0
[21] stringr_1.5.0 generics_0.1.3 vctrs_0.6.2 hms_1.1.3 bit64_4.0.5
[26] grid_4.1.2 tidyselect_1.2.0 glue_1.6.2 R6_2.5.1 fansi_1.0.4
[31] vroom_1.6.3 limma_3.50.3 farver_2.1.1 purrr_1.0.1 tidyr_1.3.0
[36] tzdb_0.4.0 ggplot2_3.4.2 magrittr_2.0.3 scales_1.2.1 codetools_0.2-19
[41] MASS_7.3-60 colorspace_2.1-0 labeling_0.4.2 utf8_1.2.3 stringi_1.7.12
[46] RCurl_1.98-1.12 munsell_0.5.0 doParallel_1.0.17 crayon_1.5.2
the backtrace returns:
Dear Tobias,
Thank you for the detailed description. Can you make available enough information for us to reproduce your problem? I.e. the script including the definitions of variables such as
tt,ll, and any required input files (they can be truncated, shortened or otherwise be made "scientifically useless" in case that's a concern).Dear Tobias, I'm afraid the current implementation cannot handle import of replicates, even though I agree that this would be highly desirable. Unfortunately, I have currently little time to develop new features in the package at the moment. If you happen to figure out the problem and a potential fix in the import function feel free to send me a pull request on GitHub: https://github.com/nkurzaw/TPP2D