Entering edit mode
Riba Michela ▴ 90
Last seen 5 months ago


I would like to deeply understand the output of the function: I have trouble in the resulting table, when I retrieve data as data.frame

When I read the resulting table I cannot reproduce the fold change with the saved values, if I use the option bNormalized=TRUE I include an example:

Chr Start   End Conc    **Conc_CD1C_POS**   **Conc_NEG**    **Fold**    p-value FDR 

sample1 sample2 sample3 sample4 sample5 sample6 Called1 Called2 102138 chr2 137707013 137707413 8,234421435 1,649371384 9,22688822 -6,20142532 1,63485E-23 2,91429E-18 0 5,76 3,65 1,649232222 745,3 331,5 720,79 9,226885788 3 3

The question is: How could be interpreted the fold and reproduced using the values reported? The problem is not present if using bNormalized=FALSE. But the fold is calculated on normalized data, right? based on the analysis method used

thanks a lot,


 dba.report(DBA, contrast, method=DBA$config$AnalysisMethod, 
           th=DBA$config$th, bUsePval=DBA$config$bUsePval, 
           fold=0, bNormalized=TRUE, bFlip=FALSE, precision,
           bCalled=FALSE, bCounts=FALSE, bCalledDetail=FALSE,
           bDB, bNotDB, bAll=TRUE, bGain=FALSE, bLoss=FALSE,

R version 4.1.1 (2021-08-10)
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/4.1/Resources/lib/libRlapack.dylib

[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_3.2.6             
 [3] SummarizedExperiment_1.22.0 Biobase_2.52.0             
 [5] MatrixGenerics_1.4.3        matrixStats_0.60.1         
 [7] GenomicRanges_1.44.0        GenomeInfoDb_1.28.2        
 [9] IRanges_2.26.0              S4Vectors_0.30.0           
[11] BiocGenerics_0.38.0        

loaded via a namespace (and not attached):
  [1] backports_1.2.1          GOstats_2.58.0          
  [3] BiocFileCache_2.0.0      plyr_1.8.6              
  [5] GSEABase_1.54.0          splines_4.1.1           
  [7] BiocParallel_1.26.2      ggplot2_3.3.5           
  [9] amap_0.8-18              digest_0.6.27           
 [11] invgamma_1.1             GO.db_3.13.0            
 [13] SQUAREM_2021.1           fansi_0.5.0             
 [15] magrittr_2.0.1           checkmate_2.0.0         
 [17] memoise_2.0.0            BSgenome_1.60.0         
 [19] base64url_1.4            limma_3.48.3            
 [21] Biostrings_2.60.2        annotate_1.70.0         
 [23] systemPipeR_1.26.3       bdsmatrix_1.3-4         
 [25] prettyunits_1.1.1        jpeg_0.1-9              
 [27] colorspace_2.0-2         blob_1.2.2              
 [29] rappdirs_0.3.3           apeglm_1.14.0           
 [31] ggrepel_0.9.1            dplyr_1.0.7             
 [33] crayon_1.4.1             RCurl_1.98-1.4          
 [35] jsonlite_1.7.2           graph_1.70.0            
 [37] genefilter_1.74.0        brew_1.0-6              
 [39] survival_3.2-13          VariantAnnotation_1.38.0
 [41] glue_1.4.2               gtable_0.3.0            
 [43] zlibbioc_1.38.0          XVector_0.32.0          
 [45] DelayedArray_0.18.0      V8_3.4.2                
 [47] Rgraphviz_2.36.0         scales_1.1.1            
 [49] pheatmap_1.0.12          mvtnorm_1.1-2           
 [51] DBI_1.1.1                edgeR_3.34.0            
 [53] Rcpp_1.0.7               xtable_1.8-4            
 [55] progress_1.2.2           emdbook_1.3.12          
 [57] bit_4.0.4                rsvg_2.1.2              
 [59] AnnotationForge_1.34.0   truncnorm_1.0-8         
 [61] httr_1.4.2               gplots_3.1.1            
 [63] RColorBrewer_1.1-2       ellipsis_0.3.2          
 [65] pkgconfig_2.0.3          XML_3.99-0.7            
 [67] dbplyr_2.1.1             locfit_1.5-9.4          
 [69] utf8_1.2.2               tidyselect_1.1.1        
 [71] rlang_0.4.11             AnnotationDbi_1.54.1    
 [73] munsell_0.5.0            tools_4.1.1             
 [75] cachem_1.0.6             generics_0.1.0          
 [77] RSQLite_2.2.8            stringr_1.4.0           
 [79] fastmap_1.1.0            yaml_2.2.1              
 [81] bit64_4.0.5              zip_2.2.0               
 [83] caTools_1.18.2           purrr_0.3.4             
 [85] KEGGREST_1.32.0          RBGL_1.68.0             
 [87] xml2_1.3.2               biomaRt_2.48.3          
 [89] compiler_4.1.1           rstudioapi_0.13         
 [91] filelock_1.0.2           curl_4.3.2              
 [93] png_0.1-7                geneplotter_1.70.0      
 [95] tibble_3.1.4             stringi_1.7.4           
 [97] GenomicFeatures_1.44.2   lattice_0.20-44         
 [99] Matrix_1.3-4             vctrs_0.3.8             
[101] pillar_1.6.2             lifecycle_1.0.0         
[103] BiocManager_1.30.16      irlba_2.3.3             
[105] data.table_1.14.0        bitops_1.0-7            
[107] rtracklayer_1.52.1       R6_2.5.1                
[109] BiocIO_1.2.0             latticeExtra_0.6-29     
[111] hwriter_1.3.2            ShortRead_1.50.0        
[113] KernSmooth_2.23-20       MASS_7.3-54             
[115] gtools_3.9.2             assertthat_0.2.1        
[117] DESeq2_1.32.0            Category_2.58.0         
[119] rjson_0.2.20             withr_2.4.2             
[121] GenomicAlignments_1.28.0 batchtools_0.9.15       
[123] Rsamtools_2.8.0          GenomeInfoDbData_1.2.6  
[125] hms_1.1.0                grid_4.1.1              
[127] DOT_0.1                  coda_0.19-4             
[129] GreyListChIP_1.24.0      ashr_2.2-47             
[131] mixsqp_0.3-43            bbmle_1.0.24            
[133] numDeriv_2016.8-1.1      restfulr_0.0.13
DiffBind • 347 views
Entering edit mode
Rory Stark ★ 4.4k
Last seen 4 days ago
CRUK, Cambridge, UK

This is a bit of a quirk really. As you say, the analysis methods compute the fold changes using normalized data, so it is not entirely clear what to report when raw data is requested.

When bNormalized=TRUE, the fold change is reported as computed by the analysis method. When bNormalized=FALSE, the fold change is computed by simply subtracting the log2 of the mean of the raw read counts across the samples in each group of the contrast. The confidence statistics (FDR) are always based on normalized data, though. I'll have a look at making this all more explicit in the help page for dba.report().

You can run the report both ways and then mix and match the metadata you are interested in (ie., the shrunken fold changes computed by DESeq2 combined with the raw read counts for each of the samples).

Entering edit mode

I thank you very much for this explanation, and for inserting in the help page in the future, It is indeed something related to the communication expecially with wet lab biologists, asking for tables where to check results, ... so thanks a lot again Michela

Entering edit mode

The man page has been updated in DiffBind_3.4.2 and subsequent versions.


Login before adding your answer.

Traffic: 892 users visited in the last hour
Help About
Access RSS

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

Powered by the version 2.3.6