Difference between revisions of "Kevinmcgee Week 13"
From LMU BioDB 2013
Kevinmcgee (Talk | contribs) (Added info to journal) |
Kevinmcgee (Talk | contribs) (Added pic) |
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[[File:LmjSampleInfo.PNG]] | [[File:LmjSampleInfo.PNG]] | ||
*Finished naming sheet with helpful names to know what is what on the sheet | *Finished naming sheet with helpful names to know what is what on the sheet | ||
| − | + | *Ready for statistical analysis | |
| − | + | *Began analysis by taking the average and standard deviation of our data chips seperately and using that information to scale and center our data: | |
=(B4-B$2)/B$3 This shows the equation we used to scale and center. | =(B4-B$2)/B$3 This shows the equation we used to scale and center. | ||
*Copied and pasted values of scaled centered onto a new page. From there, we edited out all VALUE! cells and left them blank. GenMAPP will ignore these blanks when we input our data. | *Copied and pasted values of scaled centered onto a new page. From there, we edited out all VALUE! cells and left them blank. GenMAPP will ignore these blanks when we input our data. | ||
| Line 24: | Line 24: | ||
*Created a new page titled forGENMAPP | *Created a new page titled forGENMAPP | ||
**Copied and pasted all values from statistics page | **Copied and pasted all values from statistics page | ||
| + | *Cut and pasted columns H-J and moved them to columns B-D | ||
| + | *Inserted a new column at B called System Code. Filled in column with the letter N | ||
| + | *File is now ready for GenMAPP import | ||
| + | |||
| + | |||
| + | *Sample of what the final file looked like | ||
| + | [[File:L.InfantumforGenMAPP.PNG]] | ||
Latest revision as of 19:02, 21 November 2013
- Opened L.infantumCompliedRawData(A).txt
- Finished the formatting by flipping the dye swap chips negative
- Created a column next to dye swap chips and did the formula:
=-1*(dye swap chip column)
- made a new sheet
- added all data from old sheet except only added the flipped dye swaps
- looked for background information in the array paper
- L. infantum MHOM/MA/67/ITMAP-263 and L. major LV39 MRHO/SU/59/P strains used in this study
- All microarray data will be freely available on the Geo NCBI database in the MIAME format
- The series accession number for our manuscript is GSE10407.
- Each chip compares promastigote vs. amastigote with different replicates
- Following data files found
- Finished naming sheet with helpful names to know what is what on the sheet
- Ready for statistical analysis
- Began analysis by taking the average and standard deviation of our data chips seperately and using that information to scale and center our data:
=(B4-B$2)/B$3 This shows the equation we used to scale and center.
- Copied and pasted values of scaled centered onto a new page. From there, we edited out all VALUE! cells and left them blank. GenMAPP will ignore these blanks when we input our data.
- Made a column of the average fold change for each gene call Avg_LogFC_All
Average B2:G2
- Made a column of the Tstat and Pvalue for the fold changes of each gene:
=AVERAGE(B2:G2)/STDEV(B2:G2)/SQRT(6) TStat =TDIST(ABS(I2),5,2) Pvalue
- Created a new page titled forGENMAPP
- Copied and pasted all values from statistics page
- Cut and pasted columns H-J and moved them to columns B-D
- Inserted a new column at B called System Code. Filled in column with the letter N
- File is now ready for GenMAPP import
- Sample of what the final file looked like
