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LTLA / csaw

Clone of the Bioconductor repository for the csaw package.
https://bioconductor.org/packages/devel/bioc/html/csaw.html
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mergeResults returns two FDR values in $best #12

Open malcook opened 4 years ago

malcook commented 4 years ago

Hello,

in my hands, mergeResults is returning a FDR and FDR.1 column.

I see no accounting for this in the manual and seek to understand the origin.

Can you please advise?

Example:

> mergeResults<-mergeResults(se,tt$table,tol=1)
> head(mergeResults$best)
DataFrame with 6 rows and 9 columns
       best logFC.LL_N_030...LL_N_000 logFC.LL_N_180...LL_N_000 logFC.LL_N_300...LL_N_000             logCPM                F               PValue                 FDR               FDR.1
  <integer>                 <numeric>                 <numeric>                 <numeric>          <numeric>        <numeric>            <numeric>           <numeric>           <numeric>
1    134263        -0.178801264417887       -0.0237264415049254         0.822978123641229 0.0993102288544158 3.91811182610304   0.0136863128630995  0.0672674484168762  0.0181805546839431
2     26936       -0.0603813844699492         0.150850599117195          1.42863755671713  0.397273403201469 8.74700898508821 0.000199949517631074 0.00244924426301525 0.00147077672585306
3     63972        0.0582379092041912         0.139375362767482        -0.967938604975784  0.900435518778031 6.00567783545386  0.00281101779334551   0.014498347610984 0.00733141976087592
4     26735       -0.0554056059690922         0.161113393498133         -1.29945560902003  0.986767309389848 8.66499256018883 0.000391985703402061 0.00241882743357493 0.00221665059497903
5    105898        -0.540063593372925       -0.0411272091798552        -0.900298845885423   0.20054835081267 4.55965228041453  0.00668202960401885  0.0416384017812769  0.0121138478142122
6    138186        -0.126975025787162         0.574864792202156        -0.399144244137485  0.534531681560781 3.84135763592317   0.0149270185213266  0.0712824731330411  0.0191005472169029

FWIW:

sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /n/apps/CentOS7/install/r-3.6.1/lib64/R/lib/libRblas.so
LAPACK: /n/apps/CentOS7/install/r-3.6.1/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C              LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8     LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8    LC_PAPER=en_US.utf8       LC_NAME=C                 LC_ADDRESS=C              LC_TELEPHONE=C            LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C      

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

other attached packages:
 [1] pheatmap_1.0.12             tracktables_1.20.0          Glimma_1.14.0               preprocessCore_1.48.0       purrr_0.3.3                 data.table_1.12.6           csaw_1.20.0                 SummarizedExperiment_1.16.1 DelayedArray_0.12.3         BiocParallel_1.20.0         matrixStats_0.55.0          Biobase_2.46.0              edgeR_3.28.0                limma_3.42.2                rtracklayer_1.46.0          GenomicRanges_1.38.0        GenomeInfoDb_1.22.0         IRanges_2.20.0              S4Vectors_0.24.4            BiocGenerics_0.32.0         functional_0.6             
[22] DBI_1.0.0                   scales_1.0.0                withr_2.1.2                 devtools_2.2.1              usethis_1.5.1              

loaded via a namespace (and not attached):
 [1] bitops_1.0-6             fs_1.3.1                 bit64_0.9-7              RColorBrewer_1.1-2       progress_1.2.2           httr_1.4.1               rprojroot_1.3-2          tools_3.6.1              backports_1.1.5          R6_2.4.0                 colorspace_1.4-1         tidyselect_0.2.5         prettyunits_1.0.2        processx_3.4.1           bit_1.1-14               curl_4.2                 compiler_3.6.1           reportr_1.3.0            cli_1.1.0                desc_1.2.0               callr_3.3.2              askpass_1.1              rappdirs_0.3.1          
[24] stringr_1.4.0            digest_0.6.22            Rsamtools_2.2.1          XVector_0.26.0           RNifti_0.11.1            pkgconfig_2.0.3          sessioninfo_1.1.1        dbplyr_1.4.2             rlang_0.4.1              RSQLite_2.1.2            jsonlite_1.6             dplyr_0.8.3              RCurl_1.95-4.12          magrittr_1.5             GenomeInfoDbData_1.2.2   Matrix_1.2-17            Rcpp_1.0.4.6             munsell_0.5.0            stringi_1.4.3            zlibbioc_1.32.0          pkgbuild_1.0.6           BiocFileCache_1.10.0     grid_3.6.1              
[47] blob_1.2.0               tractor.base_3.3.2       crayon_1.3.4             lattice_0.20-38          Biostrings_2.54.0        GenomicFeatures_1.38.0   hms_0.5.2                locfit_1.5-9.1           zeallot_0.1.0            ps_1.3.0                 pillar_1.4.2             biomaRt_2.42.0           pkgload_1.0.2            XML_3.98-1.20            glue_1.3.1               remotes_2.1.0            ore_1.6.3                vctrs_0.2.0              testthat_2.3.0           gtable_0.3.0             openssl_1.4.1            assertthat_0.2.1         tibble_2.1.3            
[70] GenomicAlignments_1.22.0 AnnotationDbi_1.48.0     memoise_1.1.0            ellipsis_0.3.0
LTLA commented 4 years ago

Could you try with Bioconductor 3.11 on R 4.0.0? The behavior may or may not have been already fixed there, but either way, I can't do any changes to csaw 1.20.0; that's frozen.

P.S. Note that I changed the names of some of the combineTests output fields in csaw 1.22.0 to be more general. You may need to tweak some of your downstream code if you do update.

malcook commented 4 years ago

Thanks Aaron. Alas I am not yet in a position to test in R 4.x but I expect with the forthcoming release (June 20?) I will take the upgrade and update everything. I'll circle back around on this then.

LTLA commented 4 years ago

Okay, but I'm not sure what release you're talking about; R 4.0.0's been out since April.

malcook commented 4 years ago

4.0.2https://cran.r-project.org/doc/manuals/r-patched/NEWS.pdf is slated I think for June 20 if I remember correctly

From: Aaron Lun notifications@github.com Reply-To: LTLA/csaw reply@reply.github.com Date: Monday, June 15, 2020 at 2:29 AM To: LTLA/csaw csaw@noreply.github.com Cc: Malcolm Cook MEC@stowers.org, Author author@noreply.github.com Subject: Re: [LTLA/csaw] mergeResults returns two FDR values in $best (#12)

CAUTION: This email was received from an External Source

Okay, but I'm not sure what release you're talking about; R 4.0.0's been out since April.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/LTLA/csaw/issues/12#issuecomment-643954832, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AADWHOXF7IDKJN5WTZINFYTRWXEWBANCNFSM4N4YM3QQ.