Bryan Hernandez/20.109/Lab notebook/Module 3/Day 6
--Bryanh 16:17, 25 April 2007 (EDT)
purpose: to reduce our microarray data to meaningful information with regards to gene expression.
- open txt file in xls (tab delimited)
- delete top 9 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 numerical cells as numbers with no decimal place
- we decided to consider the median variations and background. median backgrounds were subtracted from the median signal.
- 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
- Of the SAGA subunits we only saw a 1-fold increase in expression of mutant over the parent FY2068.
- we will consider negative ratios as simply 0 expression. but there werent many negative values.
- there were a good number of duplicates that agreed with each other, however I cant say much without more careful data analysis.