==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'''

**235 (4.5%) genes have a p value < 0.01

**'''235 (4.5%) genes have a p value < 0.01'''

**21 (0.4%) genes have a p value < 0.001

**'''21 (0.4%) genes have a p value < 0.001'''

**0 (0%) genes have a p value < 0.0001

**'''0 (0%) genes have a p value < 0.0001'''

*Two methods were applies in order to correct the p value and adjust it for the number of Ttests I ran. To determine how many genes fell under p value < 0.05, I filtered the data according to the values indicated in the columns indicated.

*Two methods were applies in order to correct the p value and adjust it for the number of Ttests I ran. To determine how many genes fell under p value < 0.05, I filtered the data according to the values indicated in the columns indicated.

**0 (0%) genes have a Bonferroni-corrected p value < 0.05

**'''0 (0%) genes have a Bonferroni-corrected p value < 0.05'''

**0 (0%) genes have a Benjamini and Hochberg-corrected p value < 0.05

**'''0 (0%) genes have a Benjamini and Hochberg-corrected p value < 0.05'''

*To determine which genes had a positive or negative fold change, I filtered all of the genes from the "Avg_LogFC_all" column with the indicated conditions.

*To determine which genes had a positive or negative fold change, I filtered all of the genes from the "Avg_LogFC_all" column with the indicated conditions.

**352 (6.7%) genes have a positive average log fold change in the "Avg_LogFC_all" column and a p value < 0.05

**'''352 (6.7%) genes have a positive average log fold change in the "Avg_LogFC_all" column and a p value < 0.05'''

**596 (11.4%) genes have a negative average log fold change in the "Avg_LogFC_all" column and a p value < 0.05

**'''596 (11.4%) genes have a negative average log fold change in the "Avg_LogFC_all" column and a p value < 0.05'''

**339 (6.4%) genes have an significant positive average log fold change (> 0.25) in the "Avg_LogFC_all" column and a p value < 0.05

**'''339 (6.4%) genes have an significant positive average log fold change (> 0.25) in the "Avg_LogFC_all" column and a p value < 0.05'''

**578 (11.1%) genes have an significant negative average log fold change (> 0.25) in the "Avg_LogFC_all" column and a p value < 0.05

**'''578 (11.1%) genes have an significant negative average log fold change (> 0.25) in the "Avg_LogFC_all" column and a p value < 0.05'''

*Question: What criteria did Merrell et al. (2002) use to determine a significant gene expression change? How does it compare to our method?

*Question: What criteria did Merrell et al. (2002) use to determine a significant gene expression change? How does it compare to our method?

**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.)

*VC0028 (two entries exist)

*'''VC0028 (two entries exist)'''

**Fold Change: 1.67, 1.27

**'''Fold Change: 1.67, 1.27'''

**P value: 0.0474, 0.0692

**'''P value: 0.0474, 0.0692'''

**Significantly changed? The first entry of this gene was significantly changed, but not the second.

**'''Significantly changed? The first entry of this gene was significantly changed, but not the second.'''

*VC0941 (two entries exist)

*'''VC0941 (two entries exist)'''

**Fold Change: 0.09, -0.28

**'''Fold Change: 0.09, -0.28'''

**P value: 0.6759, 0.1636

**'''P value: 0.6759, 0.1636'''

**Significantly changed? Neither entry was significantly changed.

**'''Significantly changed? Neither entry was significantly changed.'''

*VC0869 (five entries exist)

*'''VC0869 (five entries exist)'''

**Fold Change: 1.59, 1.95, 2.2, 1.5, 2.12

**'''Fold Change: 1.59, 1.95, 2.2, 1.5, 2.12'''

**P value: 0.0463, 0.0227, 0.002, 0.0174, 0.02

**'''P value: 0.0463, 0.0227, 0.002, 0.0174, 0.02'''

**Significantly changed? All entries were significantly changed.

**'''Significantly changed? All entries were significantly changed.'''

*VC0051 (two entries exist)

*'''VC0051 (two entries exist)'''

**Fold Change: 1.92, 1.89

**'''Fold Change: 1.92, 1.89'''

**P value: 0.0139, 0.016

**'''P value: 0.0139, 0.016'''

**Significantly changed? Both entries were significantly changed.

**'''Significantly changed? Both entries were significantly changed.'''

*VC0647 (three entries exist)

*'''VC0647 (three entries exist)'''

**Fold Change: -1.11, -0.94, -1.05

**'''Fold Change: -1.11, -0.94, -1.05'''

**P value: 0.0003, 0.0125, 0.0051

**'''P value: 0.0003, 0.0125, 0.0051'''

**Significantly changed? All entries were significantly changed.

**'''Significantly changed? All entries were significantly changed.'''

*VC0468 (one entry exists)

*'''VC0468 (one entry exists)'''

**Fold Change: -0.17

**'''Fold Change: -0.17'''

**P value: 0.335

**'''P value: 0.335'''

**Significantly changed? Not significantly changed.

**'''Significantly changed? Not significantly changed.'''

*VC2350 (one entry exists)

*'''VC2350 (one entry exists)'''

**Fold Change: -2.4

**'''Fold Change: -2.4'''

**P value: 0.013

**'''P value: 0.013'''

**Significantly changed? Significantly changed.

**'''Significantly changed? Significantly changed.'''

*VCA0583 (one entry exists)

*'''VCA0583 (one entry exists)'''

**Fold Change: 1.06

**'''Fold Change: 1.06'''

**P value: 0.1011

**'''P value: 0.1011'''

**Significantly changed? Not significantly changed.

**'''Significantly changed? Not significantly changed.'''

=MAPPFinder Analysis of Vibrio cholerae Microarray Data (Part 2)=

=MAPPFinder Analysis of Vibrio cholerae Microarray Data (Part 2)=

==Map Onto Biological Pathways (GenMAPP & MAPPFinder==

==Map Onto Biological Pathways (GenMAPP & MAPPFinder==

*I launched the GenMAPP software as it was installed on the lab computers in Seaver 120 as of October 20, 2015.

*I launched the GenMAPP software as it was installed on the lab computers in Seaver 120 as of October 20, 2015.