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test: test_edgeR test_DESeq2 test_voom test_PtR_PCA test_PtR_heatmap
./validate_results.pl
test_edgeR:
${TRINITY_HOME}/Analysis/DifferentialExpression/run_DE_analysis.pl -m Trinity_trans.counts.matrix --method edgeR -s samples.txt -o edgeR_outdir
cd edgeR_outdir && ${TRINITY_HOME}/Analysis/DifferentialExpression/analyze_diff_expr.pl \
--matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt && \
${TRINITY_HOME}/Analysis/DifferentialExpression/validate_UP_subset.Rscript ../samples.txt
touch test_edgeR
test_DESeq2:
${TRINITY_HOME}/Analysis/DifferentialExpression/run_DE_analysis.pl -m Trinity_trans.counts.matrix --method DESeq2 -s samples.txt -o DESeq2_outdir
cd DESeq2_outdir && ${TRINITY_HOME}/Analysis/DifferentialExpression/analyze_diff_expr.pl \
--matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt --order_columns_by_samples_file && \
${TRINITY_HOME}/Analysis/DifferentialExpression/validate_UP_subset.Rscript ../samples.txt
touch test_DESeq2
test_voom:
${TRINITY_HOME}/Analysis/DifferentialExpression/run_DE_analysis.pl -m Trinity_trans.counts.matrix --method voom -s samples.txt -o voom_outdir
cd voom_outdir && ${TRINITY_HOME}/Analysis/DifferentialExpression/analyze_diff_expr.pl \
--matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt && \
${TRINITY_HOME}/Analysis/DifferentialExpression/validate_UP_subset.Rscript ../samples.txt
touch test_voom
test_PtR_PCA:
${TRINITY_HOME}/Analysis/DifferentialExpression/PtR -m Trinity_trans.TMM.EXPR.matrix -s samples.txt --prin_comp 3 --add_prin_comp_heatmaps 30
touch test_PtR_PCA
test_PtR_heatmap:
${TRINITY_HOME}/Analysis/DifferentialExpression/PtR -m Trinity_trans.TMM.EXPR.matrix -s samples.txt --heatmap --sample_cor_matrix --log2 --save
touch test_PtR_heatmap
clean:
rm -rf ./edgeR_outdir
rm -rf ./DESeq2_outdir
rm -rf ./voom_outdir
rm -f ./Trinity_trans.counts.matrix.*
rm -f ./Trinity_trans.TMM.EXPR.matrix.*
rm -f ./*.pdf
rm -f test_edgeR test_DESeq2 test_voom test_PtR_heatmap
# in case we need to restrict tests here
#rversion := $(shell R --version | head -1)
#ifeq (,$(findstring 3.1.1, $(rversion)))
# ...
#endif
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