J'aime C. Moehlman's Week 12: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
No edit summary |
|||
| (3 intermediate revisions by the same user not shown) | |||
| Line 21: | Line 21: | ||
'''genMAPP worksheets''' | '''genMAPP worksheets''' | ||
*[[Media:Bioinformatics Merrell Compiled Raw Data Vibrio.txt|.txt file]] | *[[Media:Bioinformatics Merrell Compiled Raw Data Vibrio.txt|.txt file]] | ||
*[[Media: | *[[Media:Bioinformatics Merrell Compiled Raw Data Vibrio.xls| Excel file]] | ||
====Sanity Check==== | |||
*pvalues less than .05: 5 | |||
*pvalues less than .01: 0 | |||
*pvalues less than .001: 0 | |||
*pvalues less than .0001: 0 | |||
*Keeping the "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? | |||
**4 | |||
*Keeping the "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? | |||
**1 | |||
*There showed to be 1617 log fold changes between -.25 and .25. | |||
*Merrell et al. used the p value as criteria to determine significant gene expression change. | |||
*VC0028 has a p value of .325668 | |||
*VC0941 has a p value of about .73 | |||
*VC0869 has a p value of about .46 | |||
*VC0051 has a p value of about .28 | |||
*VC0647 has a p value of about .45 | |||
*VC0468 has a p value of about .83 | |||
*VC2350 has a p value of about .18 | |||
*VCA0583 has a p value of about .29 | |||
**These values all seem to be very different, some are significant while others don't really seem to be. | |||
{{J'aime C. Moehlman}} | |||
Latest revision as of 08:42, 20 April 2010
Vibrio cholerae Data Analysis
Normalize the log ratios for the set of slides in the experiment
- entered a new worksheet into our excel file
- pasted all of the compiled raw data into the scaled_centered worksheet
- intserted two rows at the top of the worksheet (above data & below titles)
- in cell A2, we typed "Average" and in cell A3, we typed "StdDev"
- You will now compute the Average log ratio for each chip (each column of data). We did this by using the excel equation "=AVERAGE(B4:B5224)"
- After following that example we computed the average for the rest of the columns
- Then we followed the same steps as above to compute the standard deviation of the log ratios by using the equation "=STDEV(B4:B5224)" and then found the standard deviations for all of the other columns.
- we inserted new colums to the right of each patient sample (i.e. A1- A4, B1-B4, C1-C4) and labelled them each A1-C4_scaled_centered
- In cell C4, we entered this equation: "=(B4-$B$2)/$B$3" and then did the same for every cell in the column, after that we did this for each of the following empty columns
Perform Statistical Analysis on the Ratios
- we created a new worksheet called "statistics"
- then we copied all of the gene id's into this new worksheet into column A
- we copied the values from the A1_scaled_centered worksheet
- we created 3 new columns to show the log values.
- we created a new sheet that is designed specifically for genMAPP.
genMAPP worksheets
Sanity Check
- pvalues less than .05: 5
- pvalues less than .01: 0
- pvalues less than .001: 0
- pvalues less than .0001: 0
- Keeping the "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?
- 4
- Keeping the "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?
- 1
- There showed to be 1617 log fold changes between -.25 and .25.
- Merrell et al. used the p value as criteria to determine significant gene expression change.
- VC0028 has a p value of .325668
- VC0941 has a p value of about .73
- VC0869 has a p value of about .46
- VC0051 has a p value of about .28
- VC0647 has a p value of about .45
- VC0468 has a p value of about .83
- VC2350 has a p value of about .18
- VCA0583 has a p value of about .29
- These values all seem to be very different, some are significant while others don't really seem to be.
