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Performs differential expression analyses in R between pairs of sample groups using up to 4 methods: DESeq, DESeq2, EdgeR, and upper-quartile normalization with t-test. See respective manuals for differences in method. DESeq, DESeq2 and EdgeR use raw counts as input and perform normalization internally. Similarly, upper-quartile normalization is performed prior to the t-test. In general, EdgeR and UQnorm discard 0/NA counts, but DESeq does not. The count matrix needed as input can be calculated with HTSeq, STAR, Kallisto, or any other tool for quantifying RNA-seq data.

Version 0.4
Bundle sequencing
Categories DEG Expression smallRNA
Authors Katherine Icay (katherine.icay@helsinki.fi), Alejandra Cervera (alejandra.cervera@helsinki.fi)
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Requires EdgeR (R-bioconductor) ; DESeq (R-bioconductor) ; DESeq2 (R-bioconductor) ; gtools (R-package)
Source files component.xml DE_options.r
Usage Example with default values


Name Type Mandatory Description
expr CSV Mandatory Expression matrix of raw counts. It is required that the first column must contain unique miRNA/smallRNA IDs. Column headers should contain all sample names to be evaluated. Recommended: output file of HTSeqExprMatrix.
treatment CSV Mandatory List file containing the following information: sample names (matching the column headers of the expr matrix) in the first column, and some additional column labelled "Treatment" defining the groups to be analysed. If performing pairwise analysis, an additional column "Sample" must be given. These are case-sensitive column names. NOTE: DESeq, DESeq2 will choose to analyze as the reference factor the first "Treatment" given alphabetically.


Name Type Description
array Array<CSV> Array of DEA results.
diffExpr Array<BinaryFile> Array of RData objects obtained as output of DESeq function from DESeq2 package, as output of estimateDispersions function from DESeq package and/or as output of estimateTagwiseDisp function from ergeR package.


Name Type Default Description
DE_pairwise boolean true Performs sample pairwise DE analysis. If false, DE is performed between treatment groups without looking for matched sample pairs.
options string "deseq" Comma-seperated list of possible DEAs to perform. Possible options are "deseq", "deseq2", "edgeR" and/or "uqnorm". Options are not case-sensitive, but are spelling-sensitive.
pval float 0.05 P-value cut-off for DEAs.

Test cases

Test case Parameters IN
case1 properties expr treatment array diffExpr

options=edgeR,deseq, deseq2

case2_pairwise properties expr treatment array diffExpr

options=edgeR,deseq, deseq2

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