diff --git a/_chapters/single-cell-analysis/quiz-02/index.md b/_chapters/single-cell-analysis/quiz-02/index.md index 706982f..bb36cd2 100644 --- a/_chapters/single-cell-analysis/quiz-02/index.md +++ b/_chapters/single-cell-analysis/quiz-02/index.md @@ -139,7 +139,7 @@ Map the genes in the dataset to the Entrez database. timeout={10}> - ![](sc-ex2-q8-exp.jpg) + ![](sc-ex2-q7-exp.jpg) @@ -164,6 +164,9 @@ Download the sample of a pancreas single cell gene expression dataset ([pancreas trials={2} timeout={10}> + + + ![](sc-ex2-q8-exp.jpg) @@ -201,6 +204,11 @@ b) Using Harmony widget (leave all parameters at their default values) trials={2} timeout={10}> + The t-SNE plot produced by Align Datasets shows the most effective batch correction. When colored by cell type, it displays well-defined and clearly separated clusters, indicating preservation of biological structure. At the same time, when colored by batch, the cells are well mixed across clusters, showing that batch effects have been successfully removed. + + ![](sc-ex2-q101-exp.jpg) + ![](sc-ex2-q102-exp.jpg) + ![](sc-ex2-q103-exp.jpg) @@ -225,5 +233,9 @@ Compare this plot with the previous t-SNE plot obtained using Harmony with defau trials={2} timeout={10}> + + The t-SNE plot obtained using **theta = 2.5** and **30 principal components** shows improved results compared to the default Harmony settings. Cells from different batches are better mixed, indicating more effective removal of batch effects. At the same time, clusters corresponding to cell types are more clearly separated, showing improved preservation of biological structure. + ![](sc-ex2-q111-exp.jpg) + ![](sc-ex2-q112-exp.jpg) diff --git a/_chapters/single-cell-analysis/quiz-02/sc-ex2-q10-exp.jpg b/_chapters/single-cell-analysis/quiz-02/sc-ex2-q10-exp.jpg new file mode 100644 index 0000000..de4eefd Binary files /dev/null and b/_chapters/single-cell-analysis/quiz-02/sc-ex2-q10-exp.jpg differ diff --git a/_chapters/single-cell-analysis/quiz-02/sc-ex2-q101-exp.jpg b/_chapters/single-cell-analysis/quiz-02/sc-ex2-q101-exp.jpg new file mode 100644 index 0000000..8038d5f Binary files /dev/null and b/_chapters/single-cell-analysis/quiz-02/sc-ex2-q101-exp.jpg differ diff --git a/_chapters/single-cell-analysis/quiz-02/sc-ex2-q102-exp.jpg b/_chapters/single-cell-analysis/quiz-02/sc-ex2-q102-exp.jpg new file mode 100644 index 0000000..4ef131f Binary files /dev/null and b/_chapters/single-cell-analysis/quiz-02/sc-ex2-q102-exp.jpg differ diff --git a/_chapters/single-cell-analysis/quiz-02/sc-ex2-q103-exp.jpg b/_chapters/single-cell-analysis/quiz-02/sc-ex2-q103-exp.jpg new file mode 100644 index 0000000..4aaafce Binary files /dev/null and b/_chapters/single-cell-analysis/quiz-02/sc-ex2-q103-exp.jpg differ diff --git a/_chapters/single-cell-analysis/quiz-02/sc-ex2-q111-exp.jpg b/_chapters/single-cell-analysis/quiz-02/sc-ex2-q111-exp.jpg new file mode 100644 index 0000000..48bc3c2 Binary files /dev/null and b/_chapters/single-cell-analysis/quiz-02/sc-ex2-q111-exp.jpg differ diff --git a/_chapters/single-cell-analysis/quiz-02/sc-ex2-q112-exp.jpg b/_chapters/single-cell-analysis/quiz-02/sc-ex2-q112-exp.jpg new file mode 100644 index 0000000..d2837fd Binary files /dev/null and b/_chapters/single-cell-analysis/quiz-02/sc-ex2-q112-exp.jpg differ diff --git a/_chapters/single-cell-analysis/quiz-02/sc-ex2-q7-exp.jpg b/_chapters/single-cell-analysis/quiz-02/sc-ex2-q7-exp.jpg index e13c990..3cdeba7 100644 Binary files a/_chapters/single-cell-analysis/quiz-02/sc-ex2-q7-exp.jpg and b/_chapters/single-cell-analysis/quiz-02/sc-ex2-q7-exp.jpg differ diff --git a/_chapters/single-cell-analysis/quiz-02/sc-ex2-q8-exp.jpg b/_chapters/single-cell-analysis/quiz-02/sc-ex2-q8-exp.jpg index 3cdeba7..b25c2da 100644 Binary files a/_chapters/single-cell-analysis/quiz-02/sc-ex2-q8-exp.jpg and b/_chapters/single-cell-analysis/quiz-02/sc-ex2-q8-exp.jpg differ