Claudia Campos Week 8: Difference between revisions
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'''Electronic Lab Notebook''' | |||
This Week's Analysis of Vibrio cholerae microarray data project: | |||
Mehtods: The step by step instructions | |||
Results: | |||
Interpretations: | |||
'''Sanity Check''' | '''Sanity Check''' | ||
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*What criteria did Merrell et al. (2002) use to determine a significant gene expression change? How does it compare to our method? They used the method of | *What criteria did Merrell et al. (2002) use to determine a significant gene expression change? How does it compare to our method? They used the method of | ||
*Merrell et al. (2002) report that genes with IDs: VC0028, VC0941, VC0869, VC0051, VC0647, VC0468, VC2350, and VCA0583 were all significantly changed in their data. Look these genes up in your spreadsheet? What are their fold changes and p values? Are they significantly changed in our analysis? Fold changes (respectively): 1.65, -0.28, 1.59, 1.92, -1.11, -0.17, -2.40, 1.06 P values (respectively): 0.0474, 0.1636, 0.0463, 0.0139, 0.0003, 0.3350, 0.0130, 0.1011 All except VC0941, VC0468, and VCA0583 were significantly changed since their p values were <0.05. | *Merrell et al. (2002) report that genes with IDs: VC0028, VC0941, VC0869, VC0051, VC0647, VC0468, VC2350, and VCA0583 were all significantly changed in their data. Look these genes up in your spreadsheet? What are their fold changes and p values? Are they significantly changed in our analysis? Fold changes (respectively): 1.65, -0.28, 1.59, 1.92, -1.11, -0.17, -2.40, 1.06 P values (respectively): 0.0474, 0.1636, 0.0463, 0.0139, 0.0003, 0.3350, 0.0130, 0.1011 All except VC0941, VC0468, and VCA0583 were significantly changed since their p values were <0.05. | ||
[[Media:CECfinalMerrellCompiledRawDataVibrioCCamposoct.xls | Vibiro cholerae final data in excel]] | |||
[[User:Claudia Campos | Claudia Campos]] | [[User:Claudia Campos | Claudia Campos]] | ||
[[BIOL367/F10]] | [[BIOL367/F10]] | ||
[[Category: BIOL367/F10]] | [[Category: BIOL367/F10]] | ||
Revision as of 16:30, 24 October 2010
Electronic Lab Notebook This Week's Analysis of Vibrio cholerae microarray data project: Mehtods: The step by step instructions
Results:
Interpretations:
Sanity Check
- How many genes have p value < 0.05? 5135
- What about p < 0.01? 4892
- What about p < 0.001? 1765
- What about p < 0.0001? 2
- Pvalue filter at p < 0.05, filter the "Avg_LogFC_all" column to show all genes with an average log fold change greater than zero. How many are there? 5003
- Pvalue filter at p < 0.05, filter the "Avg_LogFC_all" column to show all genes with an average log fold change less than zero. How many are there? 5063
- What about an average log fold change of > 0.25 or < -0.25? 5134
- What criteria did Merrell et al. (2002) use to determine a significant gene expression change? How does it compare to our method? They used the method of
- Merrell et al. (2002) report that genes with IDs: VC0028, VC0941, VC0869, VC0051, VC0647, VC0468, VC2350, and VCA0583 were all significantly changed in their data. Look these genes up in your spreadsheet? What are their fold changes and p values? Are they significantly changed in our analysis? Fold changes (respectively): 1.65, -0.28, 1.59, 1.92, -1.11, -0.17, -2.40, 1.06 P values (respectively): 0.0474, 0.1636, 0.0463, 0.0139, 0.0003, 0.3350, 0.0130, 0.1011 All except VC0941, VC0468, and VCA0583 were significantly changed since their p values were <0.05.
