DESeq2 followed by Reporting tools lists blank ensemble gene ID's and symbols but has image, logFC and p-value intact in HTML file
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Entering edit mode
RV • 0
@rv-10578
Last seen 4.1 years ago

Hi, 

I have been using DESeq2 and reporting tools for quite some time. I have used the [ReportingTools] HTMLReport of DESeq2 results using Ensembl Gene Ids from this post to use ensembl gene IDs to get Biomart information. I have attached the code I have been using to find that most of the ID's map to a proper gene symbol and GO id with an image, log change and p-value. But for some ID's , although I know which gene ID they belong to based on the graph's annotation, it is not getting displayed in the HTML report. I am not able to understand why if most the genes can be listed in the report, when some of them alone cannot be? 

 

Here is my R code: 

#Run the Reporting Tools
library (biomaRt)
library(ReportingTools)
mart <- useMart("ensembl",dataset="mmusculus_gene_ensembl")
add.anns <- function(df, mart, ...)
{
  nm <- rownames(df)
  anns <- getBM(attributes = c("ensembl_gene_id","external_gene_name", "description","go_id","name_1006"),
                filters = "ensembl_gene_id", values = nm, mart = mart)
  anns <- anns[match(nm, anns[, 1]), ]
  colnames(anns) <- c("ID", "Gene Symbol", "Gene Description", "GO Term Accession", "GO Term Name")
  #colnames(anns) <- c("ID", "Gene Symbol")
  df <- cbind(anns, df[, 2:ncol(df)])
  #df <- cbind(anns, df[,-1])
  rownames(df) <- nm
  df
}

htmlReport <- HTMLReport(shortName = 'RNAseq_analysis_with_DESeq2',title = 'RNA-seq analysis of differential expression using DESeq2',
                         reportDirectory = "./report")
publish (dds, factor= colData(dds)$condition, htmlReport, reportDir="./report", .modifyDF = list(add.anns, modifyReportDF), mart = mart )
#publish (res, htmlReport, reportDir="./report", mart = mart )

finish(htmlReport)

 

Here is the R session.

> sessionInfo()
R version 3.2.4 (2016-03-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.3 (Yosemite)

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     datasets  methods   base     

other attached packages:
 [1] biomaRt_2.26.1             BiocInstaller_1.20.1       RColorBrewer_1.1-2         gplots_3.0.1              
 [5] ReportingTools_2.10.0      knitr_1.12.3               org.Mm.eg.db_3.2.3         RSQLite_1.0.0             
 [9] DBI_0.3.1                  AnnotationDbi_1.32.3       calibrate_1.7.2            MASS_7.3-45               
[13] DESeq2_1.10.1              RcppArmadillo_0.6.700.3.0  Rcpp_0.12.4                SummarizedExperiment_1.0.2
[17] Biobase_2.30.0             GenomicRanges_1.22.4       GenomeInfoDb_1.6.3         IRanges_2.4.8             
[21] S4Vectors_0.8.11           BiocGenerics_0.16.1   

deseq2 rnaseq reportingtools • 804 views
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@mikelove
Last seen 15 hours ago
United States

Make sure you ping the ReportingTools maintainers by tagging with the package name.

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