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

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.