HDelgadi Week 8

Digital Lab Notebook

Continuation of classwork on Thursday October 10th [Microarray Analysis Vibrio cholerae]:

Columns B through Q were selected by highlighting the very first row of these 16 columns. Then scroll down to the last row of these columns. Hold down the 'Shift' button and highlight the entire columns. Click on the format button which is directly below the 'Delete' button under the 'Home' tab.
Click on 'Format Cells' and 'Number' under the 'Number' sub-category.
Select two decimal places and click 'OK'.
Follow steps 1 through 3 with columns R and S and select 4 decimal places rather than 2.
Select columns N through S from the very first cells, not just the values, and right click to press the 'Cut' button.
Select column B by right clicking on B and select "Insert Cut Cell" (the cells should shift 6 columns to the right).
Right click on the B header and click on 'Insert'.
The previous B column should shift one column to the right.
Under the new B header, type 'System Code' into the top cell of this column.
Below 'System Code' write the letter 'N'.
Left click on the letter 'N' and press Ctrl C to copy the letter and proceed to the last cell on the column and hold down the shift button along with left clicking this last cell (the entire column should be highlighted).
Press Ctrl V to paste the letter 'N' to all of the cells of the column.
Select File then Save As and under 'Save as type' select 'Text(Tab-delimited)(*.txt)'. Proceed to clicking OK when the signs of warnings begin to pop-up. The *.txt file is necessary to proceed.
Rename the last tab next to statistics, 'forGenMAPP', since it should have changed to the name of the file when saved as the text file.
Click on the arrow pointing down next to the A header (all columns should be highlighted at this point).
Select the 'Data' tab and click on 'Filter' (drop-down arrows should appear for each column).
Click on the drop-down arrow next to 'Pvalue'.
Click on 'Number Filters'.
Click on 'Custom Filter...' and make sure to select 'less than' on the first drop-down menu and type in 0.05 on the drop-down menu right next to it. Make sure to follow steps 17-19 for the additional respective p-values.
- Genes that have a p-value <0.05:
  1. 948 out of 5222 values
- Genes that have a p-value <.01:
  1. 235 out of 5222 values
- Genes that have a p-value <.001:
  1. 24 out of 5222 values
- Genes that have a p-value <.0001:
  1. 2 out of 5222 values
(The significance of the p-value <0.05 is that there's a significant difference in the values which demonstrates the change of gene expression)
Change the p-value to less than 0.05.
Click on the drop-down arrow next to "Avg_LogFC_all".
Click on 'Number Filters'.
Click on 'Custom Filter...'.
On the first drop-down menu make sure to select 'greater than' and type in 0 on the drop-down menu next to this one.
Follow steps 22-25 for the respective average log fold changes.
- Average log fold change greater than zero:
  1. 352
- Average log fold change less than zero:
  1. 596
- Average log fold change greater than 0.25:
  1. 339
- Average log fold change less than -0.25:
  1. 579

The Statistical Analysis for Microarrays (SAM) program was used to determine the statistically significant differences in gene expression. Merrell et al.(2002) used at least a twofold change (50% fold change) to determine these genes with statistical significant differences whereas we are using a 20% fold change.