DiffBind
1
0
Entering edit mode
Riba Michela ▴ 80
@riba-michela-6472
Last seen 20 days ago
Italy

Hi,

I am having some trouble in retrieving the results of a Differential Analysis using Diffbind. In particular, when I use the function

dba,report()

with the option bflip=TRUE or FALSE I do not see any change in the output in the field of the fold. I see a change of the column order regarding group 1 or 2 however not the fold in sense of direction of change. I can understand the values of Concentration Group 1 or 2, but not the fold, because I cannot reproduce using Group1 - Group2

as an example I write down one line of the table

Conc_a_POS Conc_NEG Fold 1,649371384 9,22688822 6,20142525

from those values: 0 5,76 3,65 # group 1

Thanks a lot if you can help me to solve

Michela


report.analysis.deseq2.df <- 
dba.report(lista.contrasti.conts.contrasts.analysis$a,method = DBA_DESEQ2,bUsePval = TRUE,th=1,fold = 0,bCounts = TRUE,bAll = TRUE,bFlip = TRUE,bNormalized = TRUE,DataType = DBA_DATA_FRAME)

sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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] parallel  stats4    stats     graphics  grDevices utils    
[7] datasets  methods   base     

other attached packages:
 [1] openxlsx_4.2.4              DiffBind_3.0.15            
 [3] SummarizedExperiment_1.20.0 Biobase_2.50.0             
 [5] MatrixGenerics_1.2.1        matrixStats_0.58.0         
 [7] GenomicRanges_1.42.0        GenomeInfoDb_1.26.7        
 [9] IRanges_2.24.1              S4Vectors_0.28.1           
[11] BiocGenerics_0.36.0        

loaded via a namespace (and not attached):
  [1] backports_1.2.1          GOstats_2.56.0          
  [3] BiocFileCache_1.14.0     plyr_1.8.6              
  [5] GSEABase_1.52.1          splines_4.0.3           
  [7] BiocParallel_1.24.1      ggplot2_3.3.4           
  [9] amap_0.8-18              digest_0.6.27           
 [11] invgamma_1.1             GO.db_3.12.1            
 [13] SQUAREM_2021.1           fansi_0.4.2             
 [15] magrittr_2.0.1           checkmate_2.0.0         
 [17] memoise_2.0.0            BSgenome_1.58.0         
 [19] base64url_1.4            limma_3.46.0            
 [21] Biostrings_2.58.0        annotate_1.68.0         
 [23] systemPipeR_1.24.3       askpass_1.1             
 [25] bdsmatrix_1.3-4          prettyunits_1.1.1       
 [27] jpeg_0.1-8.1             colorspace_2.0-0        
 [29] blob_1.2.1               rappdirs_0.3.3          
 [31] apeglm_1.12.0            ggrepel_0.9.1           
 [33] xfun_0.22                dplyr_1.0.5             
 [35] crayon_1.4.1             RCurl_1.98-1.3          
 [37] jsonlite_1.7.2           graph_1.68.0            
 [39] genefilter_1.72.1        brew_1.0-6              
 [41] survival_3.2-10          VariantAnnotation_1.36.0
 [43] glue_1.4.2               gtable_0.3.0            
 [45] zlibbioc_1.36.0          XVector_0.30.0          
 [47] DelayedArray_0.16.3      V8_3.4.0                
 [49] Rgraphviz_2.34.0         scales_1.1.1            
 [51] pheatmap_1.0.12          mvtnorm_1.1-1           
 [53] DBI_1.1.1                edgeR_3.32.1            
 [55] Rcpp_1.0.6               xtable_1.8-4            
 [57] progress_1.2.2           emdbook_1.3.12          
 [59] bit_4.0.4                rsvg_2.1                
 [61] AnnotationForge_1.32.0   truncnorm_1.0-8         
 [63] httr_1.4.2               gplots_3.1.1            
 [65] RColorBrewer_1.1-2       ellipsis_0.3.1          
 [67] pkgconfig_2.0.3          XML_3.99-0.6            
 [69] dbplyr_2.1.1             locfit_1.5-9.4          
 [71] utf8_1.2.1               tidyselect_1.1.0        
 [73] rlang_0.4.10             AnnotationDbi_1.52.0    
 [75] munsell_0.5.0            tools_4.0.3             
 [77] cachem_1.0.4             generics_0.1.0          
 [79] RSQLite_2.2.6            stringr_1.4.0           
 [81] fastmap_1.1.0            yaml_2.2.1              
 [83] knitr_1.33               bit64_4.0.5             
 [85] zip_2.1.1                caTools_1.18.2          
 [87] purrr_0.3.4              RBGL_1.66.0             
 [89] xml2_1.3.2               biomaRt_2.46.3          
 [91] compiler_4.0.3           rstudioapi_0.13         
 [93] curl_4.3                 png_0.1-8               
 [95] geneplotter_1.68.0       tibble_3.1.0            
 [97] stringi_1.5.3            GenomicFeatures_1.42.3  
 [99] lattice_0.20-41          Matrix_1.3-2            
[101] vctrs_0.3.7              pillar_1.6.0            
[103] lifecycle_1.0.0          irlba_2.3.3             
[105] data.table_1.14.0        bitops_1.0-6            
[107] rtracklayer_1.50.0       R6_2.5.0                
[109] latticeExtra_0.6-30      hwriter_1.3.2           
[111] ShortRead_1.48.0         KernSmooth_2.23-18      
[113] MASS_7.3-53.1            gtools_3.8.2            
[115] assertthat_0.2.1         DESeq2_1.30.1           
[117] openssl_1.4.3            Category_2.56.0         
[119] rjson_0.2.20             withr_2.4.1             
[121] GenomicAlignments_1.26.0 batchtools_0.9.15       
[123] Rsamtools_2.6.0          GenomeInfoDbData_1.2.4  
[125] hms_1.0.0                grid_4.0.3              
[127] DOT_0.1                  coda_0.19-4             
[129] GreyListChIP_1.22.0      ashr_2.2-47             
[131] mixsqp_0.3-43            bbmle_1.0.23.1          
[133] numDeriv_2020.2-1
bflip dba.report DiffBind • 140 views
ADD COMMENT
0
Entering edit mode
Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 4 hours ago
CRUK, Cambridge, UK

This was previously reported as a bug and fixed in version 3.2.4, so it works in the latest version of Bioconductor.

There is a workaround for version 3.0.x, which is to set the baseline for the contrast using the reorderMeta parameter of dba.contrast(). This is actually better practice -- bFlip is somewhat obsolete since version 3.0 enabled arbitrary design formulae and control of the ordering of factor values.

ADD COMMENT
0
Entering edit mode

Hi, thank you so much!

I apologize for late answering.

I'm going to update Bioconductor and follow your always kind follow up and suggestions. Hope I would be able to solve.

Thanks again,

Michela

ADD REPLY

Login before adding your answer.

Traffic: 436 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6