Carmen E. Castaneda: Week 11: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
(format entry) |
(genes and p values) |
||
Line 32: | Line 32: | ||
==== Perform statistical analysis on the ratios ==== | ==== Perform statistical analysis on the ratios ==== | ||
'''''Record the number of replacements made in your wiki page.''''' | '''''Record the number of replacements made in your wiki page.''''' | ||
*I made zero replacements in this step. | |||
==== Sanity Check: Number of genes significantly changed ==== | |||
*Answer these questions for each timepoint in your dataset. | |||
** '''How many genes have p value < 0.05?''' | |||
*For t0, there are 141 genes have a p value < 0.05. | |||
*For t10, there are 264 genes have a p value < 0.05. | |||
*For t30, there are 284 genes have a p value < 0.05. | |||
*For t120, there are 480 genes have a p value < 0.05. | |||
*For t12h, there are 387 genes have a p value < 0.05. | |||
*For t60h, there are 374 genes have a p value < 0.05. | |||
** '''What about p < 0.01?''' | |||
*For t0, there are 15 genes have a p value < 0.01. | |||
*For t10, there are 42 genes have a p value < 0.01. | |||
*For t30, there are 54 genes have a p value < 0.01. | |||
*For t120, there are 96 genes have a p value < 0.01. | |||
*For t12h, there are 87 genes have a p value < 0.01. | |||
*For t60h, there are 73 genes have a p value < 0.01. | |||
** '''What about p < 0.001?''' | |||
*For t0, there are 1 genes have a p value < 0.001. | |||
*For t10, there are 3 genes have a p value < 0.001. | |||
*For t30, there are 3 genes have a p value < 0.001. | |||
*For t120, there are 7 genes have a p value < 0.001. | |||
*For t12h, there are 8 genes have a p value < 0.001. | |||
*For t60h, there are 8 genes have a p value < 0.001. | |||
** '''What about p < 0.0001?''' | |||
*For t0, there are 0 genes have a p value < 0.0001. | |||
*For t10, there are 0 genes have a p value < 0.0001. | |||
*For t30, there are 0 genes have a p value < 0.0001. | |||
*For t120, there are 3 genes have a p value < 0.0001. | |||
*For t12h, there are 3 genes have a p value < 0.0001. | |||
*For t60h, there are 2 genes have a p value < 0.0001. |
Revision as of 22:36, 3 April 2011
Microarray Data Analysis
Background
This is a list of steps required to analyze DNA microarray data.
- Quantitate the fluorescence signal in each spot
- Calculate the ratio of red/green fluorescence
- Log transform the ratios
- Normalize the ratios on each microarray slide
- Steps 1-4 are performed by the GenePix Pro software.
- You will perform the following steps:
- Normalize the ratios for a set of slides in an experiment
- Perform statistical analysis on the ratios
- Compare individual genes with known data
- Steps 5-7 are performed in Microsoft Excel
- Pattern finding algorithms (clustering)
- Map onto biological pathways
- We will use software called STEM for the clustering and mapping
- Create mathematical model of transcriptional network
Experimental Design
For the Schade data, the timepoints are t0, t10, t30, t120, t12h (12 hours), and t60 (60 hours) of cold shock at 10°C.
- Begin by recording in your wiki the number of replicates for each time point in your data. For the group assigned to the Schade data, compare the number of replicates with what is stated in the Materials and Methods for the paper. Is it the same? If not, how is it different?
There are 3 replicates for t0, 7 replicates for t10, 6 replicates for t30, 4 replicates for t120, 4 replicates for t12h, and 6 replicates for t60h.
Normalize the ratios for a set of slides in an experiment
Why is this important?
Perform statistical analysis on the ratios
Record the number of replacements made in your wiki page.
- I made zero replacements in this step.
Sanity Check: Number of genes significantly changed
- Answer these questions for each timepoint in your dataset.
- How many genes have p value < 0.05?
- For t0, there are 141 genes have a p value < 0.05.
- For t10, there are 264 genes have a p value < 0.05.
- For t30, there are 284 genes have a p value < 0.05.
- For t120, there are 480 genes have a p value < 0.05.
- For t12h, there are 387 genes have a p value < 0.05.
- For t60h, there are 374 genes have a p value < 0.05.
- What about p < 0.01?
- For t0, there are 15 genes have a p value < 0.01.
- For t10, there are 42 genes have a p value < 0.01.
- For t30, there are 54 genes have a p value < 0.01.
- For t120, there are 96 genes have a p value < 0.01.
- For t12h, there are 87 genes have a p value < 0.01.
- For t60h, there are 73 genes have a p value < 0.01.
- What about p < 0.001?
- For t0, there are 1 genes have a p value < 0.001.
- For t10, there are 3 genes have a p value < 0.001.
- For t30, there are 3 genes have a p value < 0.001.
- For t120, there are 7 genes have a p value < 0.001.
- For t12h, there are 8 genes have a p value < 0.001.
- For t60h, there are 8 genes have a p value < 0.001.
- What about p < 0.0001?
- For t0, there are 0 genes have a p value < 0.0001.
- For t10, there are 0 genes have a p value < 0.0001.
- For t30, there are 0 genes have a p value < 0.0001.
- For t120, there are 3 genes have a p value < 0.0001.
- For t12h, there are 3 genes have a p value < 0.0001.
- For t60h, there are 2 genes have a p value < 0.0001.