Difference between revisions of "Electronic notebook: sinorhizobium meliloti"
From LMU BioDB 2013
(Created page with "==Week 12== *Read the paper on the salinity and sucrose stress on gene expression *Sorted the raw data into an XML file") |
(→Week 12) |
||
| Line 2: | Line 2: | ||
*Read the paper on the salinity and sucrose stress on gene expression | *Read the paper on the salinity and sucrose stress on gene expression | ||
*Sorted the raw data into an XML file | *Sorted the raw data into an XML file | ||
| + | *started to compile the raw data | ||
| + | |||
| + | ==Week 13== | ||
| + | *I continued to sort the raw data and began to process the data in an xls file | ||
| + | *this was a very repetitive part because it involved a lot of replications for each time set | ||
| + | *finished my compiled raw data and processed raw data, as well as the data ready for GenMAPP | ||
| + | *Made individual LOG fold change ratios for each time point replicate then averaged all of the LOG fold change ratios for each of the time points | ||
| + | *preformed a Tstat test | ||
| + | *Preformed a Pvalue test | ||
| + | *added a row of N next to the gene ID name in the forGenMAPP tab | ||
| + | *uploaded all the files to the wiki at the team page | ||
| + | |||
| + | ==week 15== | ||
| + | *I worked on some of the mistakes that I had made in my prior data sets | ||
| + | **removed AVG_LOGFC_ALL row | ||
| + | **added individual Pvalues and TSTAT for each individual replicate of the experiment instead of one Tstat and P value for the whole experiment | ||
| + | *sanity check concluded the number of genes significantly changed at each time point | ||
| + | **T15- 5520 | ||
| + | **T30- 7484 | ||
| + | **T60- 6711 | ||
| + | **T240- 5901 | ||
| + | *Removed all of the #DIV/0! from the data that was transferred over to the GenMapp data | ||
Revision as of 18:33, 3 December 2013
Week 12
- Read the paper on the salinity and sucrose stress on gene expression
- Sorted the raw data into an XML file
- started to compile the raw data
Week 13
- I continued to sort the raw data and began to process the data in an xls file
- this was a very repetitive part because it involved a lot of replications for each time set
- finished my compiled raw data and processed raw data, as well as the data ready for GenMAPP
- Made individual LOG fold change ratios for each time point replicate then averaged all of the LOG fold change ratios for each of the time points
- preformed a Tstat test
- Preformed a Pvalue test
- added a row of N next to the gene ID name in the forGenMAPP tab
- uploaded all the files to the wiki at the team page
week 15
- I worked on some of the mistakes that I had made in my prior data sets
- removed AVG_LOGFC_ALL row
- added individual Pvalues and TSTAT for each individual replicate of the experiment instead of one Tstat and P value for the whole experiment
- sanity check concluded the number of genes significantly changed at each time point
- T15- 5520
- T30- 7484
- T60- 6711
- T240- 5901
- Removed all of the #DIV/0! from the data that was transferred over to the GenMapp data
