• 00:00 1.
    index 1
  • 00:25 2.
    Question
  • 00:44 3.
    Sample Acquisition and Nucleic Acid Extraction
  • 04:12 4.
    QuestionThere were 50 µL RNA samples. You added 2 µL RNA sample to 78 µL sterile water and measured the optical density of your sample at a UV wavelength of 260 nm. If the  absorbance reading was 0.08, what was the initial amount of your RNA sample?6.4 µg
  • 05:50 5.
    Methods to Check NA Quality1
  • 07:58 6.
    QuestionWhen you check the integrity of mRNA, why do you check the integrity of ribosomal RNA (28S and 18S rRNA)?
  • 08:25 7.
    Methods to Check NA Quality2
  • 10:26 8.
    RIN-RNA Integrity Number
  • 13:16 9.
    Methods to Check NA Quality3
  • 16:45 10.
    Methods to Check RNA Quality4
  • 18:02 11.
    Steps for Microarray Experiment
  • 18:40 12.
    Sample Amplification / Labeling
  • 18:50 13.
    In Vitro Transcription
  • 19:49 14.
    Steps for Microarray Experiment
  • 20:08 15.
    Hybridization & Scanning
  • 20:24 16.
    Steps for Microarray Experiment
  • 21:18 17.
    Visual inspection of array features
  • 23:01 18.
    Box plots consist of boxes with a central line and two tailsCentral line: median of the dataUpper (seventy-fifth percentile, Q3) and lower quartile (twenty-fifth percentile, Q1) Ends of the whiskers:1.5x IQR (interquartile range) Max or min value within 1
  • 25:50 19.
    Examples of Bad Slide Quality
  • 27:30 20.
    QuestionWhat are the advantages of using Illumina bead arrays?
  • 28:47 21.
    Steps for Microarray Experiment
  • 30:09 22.
    Normalization1
  • 33:14 23.
    Normalization2
  • 36:02 24.
    Normalization3
  • 40:22 25.
    Single Channel Normalization and Scaling
  • 41:38 26.
    Summarization
  • 43:12 27.
    Visualization Tools for Microarray Analysis
  • 44:38 28.
    Heat Map and Dendrogram
  • 46:09 29.
    Violin Plot
  • 47:20 30.
    Scatter Plot
  • 49:30 31.
    MA Plot
  • 49:53 32.
    Volcano plot
  • 54:27 33.
    Bar Chart
  • 58:16 34.
    Line Graph
  • 1:00:53 35.
    Pie Chart
  • 1:01:51 36.
    Venn Diagram
  • 1:03:07 37.
    Starburst Plot
  • 1:03:59 38.
    Visualization of Gene Distribution
  • 1:06:46 39.
    Visualization of Gene Distribution
  • 1:10:06 40.
    PCA and MDS
  • 1:12:35 41.
    MDS (Multidimensional Scaling)Principal Coordinate Analysis (PCoA)
  • 1:15:11 42.
    Correspondence Analysis (CA)
  • 1:15:33 43.
    QuestionIf you want to check data quality of microarray experiments, which graph will not be used? Scatter plot of PCAHeat mapBox plotVenn diagram
  • 1:16:28 44.
    Steps for Microarray Experiment
  • 1:16:37 45.
    Precision vs Accuracy
  • 1:20:04 46.
    Confusion Matrix (混淆矩陣)
  • 1:26:33 47.
    Sensitivity vs Specificity
  • 1:27:45 48.
    Positive Predictive Value (PPV) vs Negative Predictive Value (NPV)
  • 1:28:53 49.
    Precision (PPV) vs Recall (Sensitivity)
  • 1:29:25 50.
    Accuracy Paradox
  • 1:31:53 51.
    F1 Score
  • 1:33:23 52.
    Alpha vs Beta value
  • 1:34:50 53.
    Power as a Function of Alpha and Sample Size
  • 1:37:32 54.
    Sample Size Calculation
  • 1:38:41 55.
    How to Decide the Cutpoint?
  • 1:39:44 56.
    Contradiction Between Sensitivity & Specificity
  • 1:42:59 57.
    Receiver Operating CharacteristicCurve
  • 1:45:06 58.
    Receiver Operating CharacteristicCurve
  • 1:45:41 59.
    Summary of Statistics
  • Index
  • Notes
  • Comment
  • Fullscreen
Comparative Gene-Expression Analysis I: Hybridization-based techniques (0309)
Duration: 1:47:36, Browse: 550, Last Updated: 2021-03-10
    • 00:00 1.
      index 1
    • 00:25 2.
      Question
    • 00:44 3.
      Sample Acquisition and Nucleic Acid Extraction
    • 04:12 4.
      QuestionThere were 50 µL RNA samples. You added 2 µL RNA sample to 78 µL sterile water and measured the optical density of your sample at a UV wavelength of 260 nm. If the  absorbance reading was 0.08, what was the initial amount of your RNA sample?6.4 µg
    • 05:50 5.
      Methods to Check NA Quality1
    • 07:58 6.
      QuestionWhen you check the integrity of mRNA, why do you check the integrity of ribosomal RNA (28S and 18S rRNA)?
    • 08:25 7.
      Methods to Check NA Quality2
    • 10:26 8.
      RIN-RNA Integrity Number
    • 13:16 9.
      Methods to Check NA Quality3
    • 16:45 10.
      Methods to Check RNA Quality4
    • 18:02 11.
      Steps for Microarray Experiment
    • 18:40 12.
      Sample Amplification / Labeling
    • 18:50 13.
      In Vitro Transcription
    • 19:49 14.
      Steps for Microarray Experiment
    • 20:08 15.
      Hybridization & Scanning
    • 20:24 16.
      Steps for Microarray Experiment
    • 21:18 17.
      Visual inspection of array features
    • 23:01 18.
      Box plots consist of boxes with a central line and two tailsCentral line: median of the dataUpper (seventy-fifth percentile, Q3) and lower quartile (twenty-fifth percentile, Q1) Ends of the whiskers:1.5x IQR (interquartile range) Max or min value within 1
    • 25:50 19.
      Examples of Bad Slide Quality
    • 27:30 20.
      QuestionWhat are the advantages of using Illumina bead arrays?
    • 28:47 21.
      Steps for Microarray Experiment
    • 30:09 22.
      Normalization1
    • 33:14 23.
      Normalization2
    • 36:02 24.
      Normalization3
    • 40:22 25.
      Single Channel Normalization and Scaling
    • 41:38 26.
      Summarization
    • 43:12 27.
      Visualization Tools for Microarray Analysis
    • 44:38 28.
      Heat Map and Dendrogram
    • 46:09 29.
      Violin Plot
    • 47:20 30.
      Scatter Plot
    • 49:30 31.
      MA Plot
    • 49:53 32.
      Volcano plot
    • 54:27 33.
      Bar Chart
    • 58:16 34.
      Line Graph
    • 1:00:53 35.
      Pie Chart
    • 1:01:51 36.
      Venn Diagram
    • 1:03:07 37.
      Starburst Plot
    • 1:03:59 38.
      Visualization of Gene Distribution
    • 1:06:46 39.
      Visualization of Gene Distribution
    • 1:10:06 40.
      PCA and MDS
    • 1:12:35 41.
      MDS (Multidimensional Scaling)Principal Coordinate Analysis (PCoA)
    • 1:15:11 42.
      Correspondence Analysis (CA)
    • 1:15:33 43.
      QuestionIf you want to check data quality of microarray experiments, which graph will not be used? Scatter plot of PCAHeat mapBox plotVenn diagram
    • 1:16:28 44.
      Steps for Microarray Experiment
    • 1:16:37 45.
      Precision vs Accuracy
    • 1:20:04 46.
      Confusion Matrix (混淆矩陣)
    • 1:26:33 47.
      Sensitivity vs Specificity
    • 1:27:45 48.
      Positive Predictive Value (PPV) vs Negative Predictive Value (NPV)
    • 1:28:53 49.
      Precision (PPV) vs Recall (Sensitivity)
    • 1:29:25 50.
      Accuracy Paradox
    • 1:31:53 51.
      F1 Score
    • 1:33:23 52.
      Alpha vs Beta value
    • 1:34:50 53.
      Power as a Function of Alpha and Sample Size
    • 1:37:32 54.
      Sample Size Calculation
    • 1:38:41 55.
      How to Decide the Cutpoint?
    • 1:39:44 56.
      Contradiction Between Sensitivity & Specificity
    • 1:42:59 57.
      Receiver Operating CharacteristicCurve
    • 1:45:06 58.
      Receiver Operating CharacteristicCurve
    • 1:45:41 59.
      Summary of Statistics
    Location
    Folder name
    2021
    Author
    賴亮全
    Branch
    賴亮全教授
    Created
    2021-03-09 16:21:10
    Last Updated
    2021-03-10 13:43:59
    Duration
    1:47:36