20.109(S07): Microarray data analysis: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
No edit summary |
No edit summary |
||
| Line 3: | Line 3: | ||
==Introduction== | ==Introduction== | ||
==Protocols== | ==Protocols== | ||
Here is a rough outline of the steps you can take to examine your microarray data. There are many variations on this that are acceptable and that may be more interesting or appropriate for you. You should explore the data as you see fit. | |||
#open txt file in xls (tab delimited) | |||
#delete top 21 rows | |||
#label a new worksheet for working with your data | |||
#copy columns for: GeneName, SystematicName, Description, gMeanSignal, rMeanSignal gMedianSignal, rMedianSignal, gBGMeanSignal, rBGMeanSignal, gBGMedianSignal, rBGMedianSignal | |||
#format the numberical cells as numbers with no decimal place | |||
#consider mean and median variations and background, to correct as you see fit. Be sure you keep track in your notebook or in the xls file of your analytical decisions. | |||
#start new column with ratio of green signal/red signal. | |||
#start new column called log2green/red and use data in green/red column as =LOG(cell#,base), for example =LOG(D3,2) and drag corner to apply formula to all 11K cells. Again format to whole numbers if this does not happen automatically. | |||
#Select entire sheet by clicking on diamond in corner then sort by log2 (green/red). | |||
#Sort cells in decending order according to log2green/red | |||
#What do you see? Are the duplicates in agreement? Are there particular genes you expect to see up or down regulated in the two samples (e.g. URA3)? What happens to the SAGA-subunits? Are there particular kinds of genes (e.g. mating type genes, gal regualated genes...) that are up or down regulated by the deletion? Ask the questions you want about this data... | |||
#save as XLS worksheet or workbook | |||
DONE! | DONE! | ||
==For next time== | ==For next time== | ||
Your first draft of your Mod 3 lab report is due next time. | |||
Revision as of 08:51, 8 January 2007
Introduction
Protocols
Here is a rough outline of the steps you can take to examine your microarray data. There are many variations on this that are acceptable and that may be more interesting or appropriate for you. You should explore the data as you see fit.
- open txt file in xls (tab delimited)
- delete top 21 rows
- label a new worksheet for working with your data
- copy columns for: GeneName, SystematicName, Description, gMeanSignal, rMeanSignal gMedianSignal, rMedianSignal, gBGMeanSignal, rBGMeanSignal, gBGMedianSignal, rBGMedianSignal
- format the numberical cells as numbers with no decimal place
- consider mean and median variations and background, to correct as you see fit. Be sure you keep track in your notebook or in the xls file of your analytical decisions.
- start new column with ratio of green signal/red signal.
- start new column called log2green/red and use data in green/red column as =LOG(cell#,base), for example =LOG(D3,2) and drag corner to apply formula to all 11K cells. Again format to whole numbers if this does not happen automatically.
- Select entire sheet by clicking on diamond in corner then sort by log2 (green/red).
- Sort cells in decending order according to log2green/red
- What do you see? Are the duplicates in agreement? Are there particular genes you expect to see up or down regulated in the two samples (e.g. URA3)? What happens to the SAGA-subunits? Are there particular kinds of genes (e.g. mating type genes, gal regualated genes...) that are up or down regulated by the deletion? Ask the questions you want about this data...
- save as XLS worksheet or workbook
DONE!
For next time
Your first draft of your Mod 3 lab report is due next time.
