Example results

On this page we have collected example results obtained by applying the differential expression analysis methods interfaced by compcodeR to the benchmarking data sets. Note that the files are large! Please note also that the results may be updated following updates of the differential expression methods, and that new methods may be added. However, there is no guarantee that the results available from this page will always correspond to the latest version of the methods. All information regarding version numbers etc. are available in the result objects. Please consult the vignette or the manual for more information about how to apply your own favorite method to the benchmarking data.

Bottomly

Method Date Link
All methods 19/11 2013 download
baySeq 19/11 2013 download
DESeq (nbinom, GLM) 19/11 2013 download
DESeq2 19/11 2013 download
DSS 19/11 2013 download
edgeR (exact, GLM), TCC 19/11 2013 download
HTSDiff 19/11 2013 download
limma (+voom, vst, logcpm, sqrtcpm) 19/11 2013 download
NBPSeq 19/11 2013 download
NOISeq 19/11 2013 download
SAMseq 19/11 2013 download
t-test (+voom, vst, raw) 19/11 2013 download

BottomlySingleStrain

Method Date Link
All methods 19/11 2013 download
baySeq 19/11 2013 download
DESeq (nbinom, GLM) 19/11 2013 download
DSS 19/11 2013 download
edgeR (exact, GLM), TCC 19/11 2013 download
HTSDiff 19/11 2013 download
limma (+voom, vst, logcpm, sqrtcpm) 19/11 2013 download
NBPSeq 19/11 2013 download
NOISeq 19/11 2013 download
SAMseq 19/11 2013 download
t-test (+voom, vst, raw) 19/11 2013 download

Gilad

Method Date Link
All methods 19/11 2013 download
baySeq 19/11 2013 download
DESeq (nbinom, GLM) 19/11 2013 download
DESeq2 19/11 2013 download
DSS 19/11 2013 download
edgeR (exact, GLM), TCC 19/11 2013 download
HTSDiff 19/11 2013 download
limma (+voom, vst, logcpm, sqrtcpm) 19/11 2013 download
NBPSeq 19/11 2013 download
NOISeq 19/11 2013 download
SAMseq 19/11 2013 download
t-test (+voom, vst, raw) 19/11 2013 download

Hammer

Method Date Link
All methods 19/11 2013 download
baySeq 19/11 2013 download
DESeq (nbinom, GLM) 19/11 2013 download
DESeq2 19/11 2013 download
DSS 19/11 2013 download
edgeR (exact, GLM), TCC 19/11 2013 download
HTSDiff 19/11 2013 download
limma (+voom, vst, logcpm, sqrtcpm) 19/11 2013 download
NBPSeq 19/11 2013 download
NOISeq 19/11 2013 download
SAMseq 19/11 2013 download
t-test (+voom, vst, raw) 19/11 2013 download

NB_0_0

Method Date Link
All methods 19/11 2013 download
baySeq 19/11 2013 download
DESeq (nbinom, GLM) 19/11 2013 download
DSS 19/11 2013 download
edgeR (exact, GLM), TCC 19/11 2013 download
HTSDiff 19/11 2013 download
limma (+voom, vst, logcpm, sqrtcpm) 19/11 2013 download
NBPSeq 19/11 2013 download
NOISeq 19/11 2013 download
SAMseq 19/11 2013 download
t-test (+voom, vst, raw) 19/11 2013 download

NB_625_625

Method Date Link
All methods 19/11 2013 download
baySeq 19/11 2013 download
DESeq (nbinom, GLM) 19/11 2013 download
DESeq2 19/11 2013 download
DSS 19/11 2013 download
edgeR (exact, GLM), TCC 19/11 2013 download
HTSDiff 19/11 2013 download
limma (+voom, vst, logcpm, sqrtcpm) 19/11 2013 download
NBPSeq 19/11 2013 download
NOISeq 19/11 2013 download
SAMseq 19/11 2013 download
t-test (+voom, vst, raw) 19/11 2013 download

NB_625_625_diffdisp

Method Date Link
All methods 19/11 2013 download
baySeq 19/11 2013 download
DESeq (nbinom, GLM) 19/11 2013 download
DSS 19/11 2013 download
edgeR (exact, GLM), TCC 19/11 2013 download
HTSDiff 19/11 2013 download
limma (+voom, vst, logcpm, sqrtcpm) 19/11 2013 download
NBPSeq 19/11 2013 download
NOISeq 19/11 2013 download
SAMseq 19/11 2013 download
t-test (+voom, vst, raw) 19/11 2013 download

NB_1250_0

Method Date Link
All methods 19/11 2013 download
baySeq 19/11 2013 download
DESeq (nbinom, GLM) 19/11 2013 download
DESeq2 19/11 2013 download
DSS 19/11 2013 download
edgeR (exact, GLM), TCC 19/11 2013 download
HTSDiff 19/11 2013 download
limma (+voom, vst, logcpm, sqrtcpm) 19/11 2013 download
NBPSeq 19/11 2013 download
NOISeq 19/11 2013 download
SAMseq 19/11 2013 download
t-test (+voom, vst, raw) 19/11 2013 download

NB_2000_2000

Method Date Link
All methods 19/11 2013 download
DESeq2 19/11 2013 download
DSS 19/11 2013 download
edgeR (GLM), TCC 19/11 2013 download
limma (+voom) 19/11 2013 download
NBPSeq 19/11 2013 download
SAMseq 19/11 2013 download
t-test (raw) 19/11 2013 download

NB_4000_0

Method Date Link
All methods 19/11 2013 download
DESeq2 19/11 2013 download
DSS 19/11 2013 download
edgeR (GLM), TCC 19/11 2013 download
limma (+voom) 19/11 2013 download
NBPSeq 19/11 2013 download
SAMseq 19/11 2013 download
t-test (raw) 19/11 2013 download

P_625_625

Method Date Link
All methods 19/11 2013 download
baySeq 19/11 2013 download
DESeq (nbinom, GLM) 19/11 2013 download
DSS 19/11 2013 download
edgeR (exact, GLM), TCC 19/11 2013 download
HTSDiff 19/11 2013 download
limma (+voom, vst, logcpm, sqrtcpm) 19/11 2013 download
NBPSeq 19/11 2013 download
NOISeq 19/11 2013 download
SAMseq 19/11 2013 download
t-test (+voom, vst, raw) 19/11 2013 download

R_625_625

Method Date Link
All methods 19/11 2013 download
baySeq 19/11 2013 download
DESeq (nbinom, GLM) 19/11 2013 download
DSS 19/11 2013 download
edgeR (exact, GLM), TCC 19/11 2013 download
HTSDiff 19/11 2013 download
limma (+voom, vst, logcpm, sqrtcpm) 19/11 2013 download
NBPSeq 19/11 2013 download
NOISeq 19/11 2013 download
SAMseq 19/11 2013 download
t-test (+voom, vst, raw) 19/11 2013 download

S_625_625

Method Date Link
All methods 19/11 2013 download
baySeq 19/11 2013 download
DESeq (nbinom, GLM) 19/11 2013 download
DESeq2 19/11 2013 download
DSS 19/11 2013 download
edgeR (exact, GLM), TCC 19/11 2013 download
HTSDiff 19/11 2013 download
limma (+voom, vst, logcpm, sqrtcpm) 19/11 2013 download
NBPSeq 19/11 2013 download
NOISeq 19/11 2013 download
SAMseq 19/11 2013 download
t-test (+voom, vst, raw) 19/11 2013 download