Difference between revisions of "Kevinmcgee Week 8"
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Digital Notebook | Digital Notebook | ||
| + | |||
| + | =='''Part 1'''== | ||
| + | |||
#Downloaded the Stanford Microarray Database data. | #Downloaded the Stanford Microarray Database data. | ||
#Made a new page called scaled_centered. Copied data from previous page, and calculated average ( =AVERAGE(B4:B5224) ) and standard deviation ( =STDEV(B4:B5224) )of them. | #Made a new page called scaled_centered. Copied data from previous page, and calculated average ( =AVERAGE(B4:B5224) ) and standard deviation ( =STDEV(B4:B5224) )of them. | ||
| Line 6: | Line 9: | ||
#Made page called forGenMAPP. On this page, pasted statistics page, then prepared for GenMAPP (number of decimal places, location of some column of information). | #Made page called forGenMAPP. On this page, pasted statistics page, then prepared for GenMAPP (number of decimal places, location of some column of information). | ||
| + | =='''Part 2'''== | ||
| + | |||
| + | #121 Errors found | ||
| + | #*My partner had 722 errors. The reason that he has more errors could be that he used an older version of the database, meaning that genes not found in his database could have been added since the last update. | ||
| + | #The first 10 terms are as follows: | ||
| + | #*biological adhesion | ||
| + | #*biological regulation | ||
| + | #*carbon utilization | ||
| + | #*cell killing | ||
| + | #*cellular component organization or biogenesis | ||
| + | #*cellular component organization | ||
| + | #*cell projection organization | ||
| + | #*cell projection assembly | ||
| + | #*flagellum organization | ||
| + | #*pilus organization | ||
| + | ##*The lists are different from one another. This could be because I am using a database from 2012 while my buddy is using one from 2008 | ||
| + | #Gene associated Go terms | ||
| + | #*VC0028 | ||
| + | ##*metal ion binding | ||
| + | ##*ion sulfur cluster binding | ||
| + | ##* 4 iron, 4 sulfur cluster binding | ||
| + | ##*catalytic activity | ||
| + | ##*lyase activity | ||
| + | #*VC0941 | ||
| + | ##*transferase activity | ||
| + | ##*glycine hydroxymethyltransferase activity | ||
| + | ##*Catalyitic activity | ||
| + | ##*pyridoxyl phosphate bonding | ||
| + | #*VC0869 | ||
| + | ##*ligase activity | ||
| + | ##*catalytic activity | ||
| + | ##*ATP binding | ||
| + | ##*nucleotide binding | ||
| + | #*VC0051 | ||
| + | ##*catalytic activity | ||
| + | ##*ATP binding | ||
| + | ##*nucleotide binding | ||
| + | #*VC0647 | ||
| + | ##*transferase activity | ||
| + | ##*nucleotidyltransferase activity | ||
| + | ##*RNA binding | ||
| + | ##*exribonuclease activity | ||
| + | ##*mitochondriaon | ||
| + | #*VC0468 | ||
| + | ##*catalytic activity | ||
| + | ##*ATP binding | ||
| + | ##*nucleotide binding | ||
| + | #*VC2350 | ||
| + | ##*nothing was found | ||
| + | #*VCA0583 | ||
| + | ##*Outer membrane-bounded periplasmic space | ||
| + | #*'''Are they the same as your buddy? why or why not?''' | ||
| + | # | ||
*[[Media: Merrell_Compiled_Raw_Data_Vibrio_KevinMcGee_10132013.txt|.txt spreadsheet]] | *[[Media: Merrell_Compiled_Raw_Data_Vibrio_KevinMcGee_10132013.txt|.txt spreadsheet]] | ||
Revision as of 17:45, 17 October 2013
Digital Notebook
Part 1
- Downloaded the Stanford Microarray Database data.
- Made a new page called scaled_centered. Copied data from previous page, and calculated average ( =AVERAGE(B4:B5224) ) and standard deviation ( =STDEV(B4:B5224) )of them.
- Made column for each called scaled_centered which subtracts average and divides by standard deviation ( =(B4-B$2)/B$3 ).
- Made a new sheet called statistics. Copied data from previous page and took the average log fold change for each id value(=AVERAGE(B2:E2)). We then made a Tstat column which tells us if the scaled or centered average log ratio has change ( =AVERAGE(N2:P2)/(STDEV(N2:P2)/SQRT(3) ) ). Finally, made a column for Pvalue ( =TDIST(ABS(R2),2,2) ).
- Made page called forGenMAPP. On this page, pasted statistics page, then prepared for GenMAPP (number of decimal places, location of some column of information).
Part 2
- 121 Errors found
- My partner had 722 errors. The reason that he has more errors could be that he used an older version of the database, meaning that genes not found in his database could have been added since the last update.
- The first 10 terms are as follows:
- biological adhesion
- biological regulation
- carbon utilization
- cell killing
- cellular component organization or biogenesis
- cellular component organization
- cell projection organization
- cell projection assembly
- flagellum organization
- pilus organization
- The lists are different from one another. This could be because I am using a database from 2012 while my buddy is using one from 2008
- Gene associated Go terms
- VC0028
- metal ion binding
- ion sulfur cluster binding
- 4 iron, 4 sulfur cluster binding
- catalytic activity
- lyase activity
- VC0941
- transferase activity
- glycine hydroxymethyltransferase activity
- Catalyitic activity
- pyridoxyl phosphate bonding
- VC0869
- ligase activity
- catalytic activity
- ATP binding
- nucleotide binding
- VC0051
- catalytic activity
- ATP binding
- nucleotide binding
- VC0647
- transferase activity
- nucleotidyltransferase activity
- RNA binding
- exribonuclease activity
- mitochondriaon
- VC0468
- catalytic activity
- ATP binding
- nucleotide binding
- VC2350
- nothing was found
- VCA0583
- Outer membrane-bounded periplasmic space
- Are they the same as your buddy? why or why not?
