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.

protocols

 * 1) open txt file in xls (tab delimited)
 * 2) delete top 9 rows
 * 3) label a new worksheet for working with your data
 * 4) copy columns for: GeneName, SystematicName, Description, gMeanSignal, rMeanSignal	gMedianSignal, rMedianSignal, gBGMeanSignal, rBGMeanSignal, gBGMedianSignal, rBGMedianSignal
 * 5) format the numerical cells as numbers with no decimal place
 * 6) we decided to consider the median variations and background. median backgrounds were subtracted from the median signal.
 * 7) start new column with ratio of green signal/red signal.
 * 8) 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.
 * 9) Select entire sheet by clicking on diamond in corner then sort by log2 (green/red).
 * 10) Sort cells in decending order according to log2green/red

summary

 * 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.