├── .gitignore ├── Advanced_data_manipulation.Rmd ├── Advanced_data_manipulation.html ├── Advanced_data_manipulation.md ├── Advanced_graphics_in_R.Rmd ├── Advanced_graphics_in_R.html ├── Advanced_graphics_in_R.md ├── Advanced_graphics_in_R_files └── figure-html │ ├── boxplots-1.png │ ├── ggplot-iris-1.png │ ├── ggplot-iris-suite-1.png │ ├── ggplot-themes-1.png │ ├── ggthemes-1.png │ ├── ggthemes2-1.png │ ├── histogram-1.png │ ├── multi-facet-1.png │ ├── plot-1.png │ ├── qplot-on-iris-1.png │ ├── qplot-on-iris-boxplot-1.png │ ├── qplot-on-iris-boxplot-aes-1.png │ ├── qplot-on-iris-df-1.png │ ├── qplot-on-iris-line-1.png │ ├── qplot-on-iris-point-1.png │ ├── qplot-on-iris-point-line-1.png │ ├── qplot-on-iris-scatter-aes-1.png │ ├── qplot-on-iris-scatter-facet-1.png │ └── qplot-on-iris-scatter-facet2-1.png ├── Batch_effects.Rmd ├── Batch_effects.html ├── Batch_effects.md ├── Bioconductor_intro.Rmd ├── Bioconductor_intro.html ├── Bioconductor_intro.md ├── Biology_basics.Rmd ├── Biology_basics.html ├── Biology_basics.md ├── Data ├── GEO │ └── README.md └── SDY61 │ ├── SDY61.sqlite │ ├── arm_2_subject.txt │ ├── arm_or_cohort.txt │ ├── biosample.txt │ └── hai_result.txt ├── Differential_expression.Rmd ├── Differential_expression.html ├── Differential_expression.md ├── Differential_expression_files └── figure-html │ ├── unnamed-chunk-10-1.png │ ├── unnamed-chunk-12-1.png │ └── unnamed-chunk-2-1.png ├── Final-project.md ├── GSEA-sets ├── BTM_for_GSEA_20131008.gmt └── c2.all.v4.0.symbols.gmt ├── GSEA.Rmd ├── GSEA.html ├── GSEA.md ├── GSEA_files └── figure-html │ ├── .unnamed-chunk-12-1.png-lmas │ ├── unnamed-chunk-10-1.png │ ├── unnamed-chunk-12-1.png │ ├── unnamed-chunk-13-1.png │ └── unnamed-chunk-16-1.png ├── HW1.md ├── HW2.md ├── HW3.md ├── HW4.md ├── Images ├── Affy-probe.png ├── Anova.png ├── Dchip.png ├── Design-dyeswap.png ├── Design.png ├── Error-rate.png ├── GC-bias.png ├── GC-effect.png ├── Lack-of-fit.png ├── Lowess-scale.png ├── Lowess.png ├── MAS-4.0.png ├── MAS-5.0.png ├── Naive-summary-array.png ├── Naive-summary.png ├── PICS1.png ├── PICS2.png ├── PICS3.png ├── PICS4.png ├── PICS5.png ├── PICS6.png ├── PICS7.png ├── PICS8.png ├── PICS9.png ├── PM-MM-probes.png ├── Positional-model.png ├── Printip.png ├── RMA-background.png ├── RMA-model.png ├── RNA-seq-workflow.png ├── RT.png ├── TMM-formula.png ├── TMM-motivation.png ├── Wu-Naef.png ├── affymetrix-image.png ├── affymetrix-layout.png ├── affymetrix-protocol.png ├── after-quantile.png ├── before-quantile.png ├── cDNA-microarrays.png ├── dChip-fit.png ├── gcRMA-MAS-RMA.png ├── hybridization.png ├── journal.pcbi.1002276.g001.png ├── microarray-image.png ├── probe-set.png └── quantile-density.png ├── Installing_Bioinformatics_Tools.Rmd ├── Installing_Bioinformatics_Tools.html ├── Installing_Bioinformatics_Tools.md ├── Introduction_to_R.Rmd ├── Introduction_to_R.html ├── Introduction_to_R.md ├── LICENSE ├── Lab3_QA_Server_HW_Projects.Rmd ├── Lab_Searching_GEO.Rmd ├── Lab_Searching_GEO.html ├── Lab_Searching_GEO.md ├── Microarrays.Rmd ├── Microarrays.html ├── Microarrays.md ├── Midterm.html ├── Midterm.md ├── Midterm_new.html ├── Midterm_new.md ├── Normalization.Rmd ├── Normalization.html ├── Normalization.md ├── Prediction.Rmd ├── Prediction.html ├── Prediction.md ├── Prediction_files └── figure-html │ ├── unnamed-chunk-12-1.png │ ├── unnamed-chunk-13-1.png │ ├── unnamed-chunk-16-1.png │ ├── unnamed-chunk-18-1.png │ ├── unnamed-chunk-19-1.png │ ├── unnamed-chunk-5-1.png │ └── unnamed-chunk-6-1.png ├── Probe_summary.Rmd ├── Probe_summary.html ├── Probe_summary.md ├── README.md ├── RNA-seq.Rmd ├── RNA-seq.html ├── RNA-seq.md ├── RNA-seq_files └── figure-html │ ├── unnamed-chunk-8-1.png │ └── unnamed-chunk-9-1.png ├── Sequence_analysis.Rmd ├── Sequence_analysis.html ├── Sequence_analysis.md ├── Sequence_analysis_files └── figure-html │ ├── unnamed-chunk-18-1.png │ ├── unnamed-chunk-30-1.png │ └── unnamed-chunk-43-1.png ├── Using_RSEM.Rmd ├── 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