*[[Media:Week8HW-AV.zip|All Files for Week 8 Journal]]

*[[Media:Week8HW-AV.zip|All Files for Week 8 Journal]]

* '''The below instructions are adapted from the [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae Sample Microarray Analysis for ''Vibrio cholerae'' page] and the [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols GenMAPP and MAPPFinder Protocols page] hosted by [http://www.openwetware.org OpenWetWare.org].'''

* '''The below instructions are adapted from the [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae Sample Microarray Analysis for ''Vibrio cholerae'' page] and the [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols GenMAPP and MAPPFinder Protocols page] hosted by [http://www.openwetware.org OpenWetWare.org].'''

==Statistical Analysis of Vibrio cholerae Microarray Data (Part 1)==

=Statistical Analysis of Vibrio cholerae Microarray Data (Part 1)=

*First, I downloaded the Merrell_Compiled_Raw_Data_Vibrio.xls|Merrell_Compiled_Raw_Data_Vibrio.xls file to my Desktop and saved a copy with my initials and the current date. (This file can be accessed on the [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae page containing the procedure for part 1] or in the .zip file uploaded at the top of this lab assignment.

*First, I downloaded the Merrell_Compiled_Raw_Data_Vibrio.xls|Merrell_Compiled_Raw_Data_Vibrio.xls file to my Desktop and saved a copy with my initials and the current date. (This file can be accessed on the [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae page containing the procedure for part 1] or in the .zip file uploaded at the top of this lab assignment.

===Normalize the log ratios for the set of slides in the experiment===

==Normalize the log ratios for the set of slides in the experiment==

*I created a new Worksheet in my Excel file and named it "scaled_centered"

*I created a new Worksheet in my Excel file and named it "scaled_centered"

*I transferred all of the data in the "complied_raw_data" worksheet into the "scaled_centered" worksheet  

*I transferred all of the data in the "complied_raw_data" worksheet into the "scaled_centered" worksheet  

*I repeated this step for all of the "_scaled_centered" columns

*I repeated this step for all of the "_scaled_centered" columns

===Perform statistical analysis on the ratios===

==Perform statistical analysis on the ratios==

*After creating a new worksheet called "statistics", I copied and pasted the "ID" column from the "scaled_centered" worksheet  

*After creating a new worksheet called "statistics", I copied and pasted the "ID" column from the "scaled_centered" worksheet  

*I then copied over all of the "_scaled_centered" columns from the "scaled_centered" sheet into the "statistics" sheet using Past Special>Values, and deleted the rows titled "Average" and "StDev"

*I then copied over all of the "_scaled_centered" columns from the "scaled_centered" sheet into the "statistics" sheet using Past Special>Values, and deleted the rows titled "Average" and "StDev"

*In this column, I calculated the P value using the equation: <code>=TDIST(ABS(R2),degrees of freedom,2)</code>

*In this column, I calculated the P value using the equation: <code>=TDIST(ABS(R2),degrees of freedom,2)</code>

====Calculate the Bonferroni p value correction====

===Calculate the Bonferroni p value correction===

*I created two columns to the right of the "Pval" column and named both of them "Bonferroni_Pvalue"

*I created two columns to the right of the "Pval" column and named both of them "Bonferroni_Pvalue"

*In the first column, I wrote the equation <code>=S2*5221</code> in the first row and then copied the formula throughout the column

*In the first column, I wrote the equation <code>=S2*5221</code> in the first row and then copied the formula throughout the column

*In the second column, I created a condition that replaced any p value greater than 1 with a 1 using the equation <code>=IF(T2>1,1,T2)</code>

*In the second column, I created a condition that replaced any p value greater than 1 with a 1 using the equation <code>=IF(T2>1,1,T2)</code>

====Calculate the Benjamini & Hochberg p value Correction====

===Calculate the Benjamini & Hochberg p value Correction===

*I created a new worksheet called "B-H_Pvaue"  

*I created a new worksheet called "B-H_Pvaue"  

**This is important because we will be reordering the data and we want to prevent the rest of the sheet from being affected by the calculations required for the B-H p value

**This is important because we will be reordering the data and we want to prevent the rest of the sheet from being affected by the calculations required for the B-H p value

*I then selected columns A through F and reordered them in ascending order by the Master Index and copies the last "B-H_Pvalue" column into my "statistics" sheet

*I then selected columns A through F and reordered them in ascending order by the Master Index and copies the last "B-H_Pvalue" column into my "statistics" sheet

====Prepare file for GenMAPP====

===Prepare file for GenMAPP===

*A new sheet was created and named "forGenMAPP"

*A new sheet was created and named "forGenMAPP"

*Everything was copied from the statistics sheet into this sheet using Paste Special>Values

*Everything was copied from the statistics sheet into this sheet using Paste Special>Values

*This worksheet was saved as a tab delimited *.txt file

*This worksheet was saved as a tab delimited *.txt file

===Sanity Check: Number of genes significantly change===

==Sanity Check: Number of genes significantly change==

*To determine how many genes fall under each pvalue category, I added a filter to all rows of data and filtered the data according to the values indicated.

*To determine how many genes fall under each pvalue category, I added a filter to all rows of data and filtered the data according to the values indicated.

**948 (18.2%) genes have a p value < 0.05

**948 (18.2%) genes have a p value < 0.05

**Merrell et al. determined statistically significant differences in gene expression using the Statistical Analysis for Microarrays (SAM) program. According to the article, genes that were determined to have statistically significant change were genes that had at least a two fold change in expression. Our method used p values to test for significant differences between experimental and control data.  

**Merrell et al. determined statistically significant differences in gene expression using the Statistical Analysis for Microarrays (SAM) program. According to the article, genes that were determined to have statistically significant change were genes that had at least a two fold change in expression. Our method used p values to test for significant differences between experimental and control data.  

===Sanity Check: Compare individual genes with known data===

==Sanity Check: Compare individual genes with known data==

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. However, in our data...

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. However, in our data...

*(All genes were checked by searching the gene name in the "ID" column of the Excel spreadsheet.)

*(All genes were checked by searching the gene name in the "ID" column of the Excel spreadsheet.)

**Significantly changed?

**Significantly changed?