Difference between revisions of "Talk:Team Name"

Revision as of 23:46, 26 November 2013

Feedback for Miles

Text of e-mail sent on 9/26/13 3:46PM:

Dear Miles,

I reviewed the file you linked to below. There are a couple of things that need to be fixed before you can go on.

In the sheet labeled statistics, you need to get rid of the column "AVG_LOGFC_ALL". You do not need to calculate this average for your dataset. We did this for the Vibrio data because we first averaged the technical replicates then we averaged the biological replicates. In your experimental design, you have four timepoints that each has three biological replicates. So you need an average for each timepoint, but it doesn't make sense to average all the timepoints together.

Therefore, you need to also compute a TSTAT and p value for each timepoint separately. For example, the TSTAT for the 15 minute timepoint would be

=AVERAGE(B2:D2)/(STDEV(B2:D2)/SQRT(3))  

You would need to then create formulas like this for the 30, 60 and 240 timepoints. You would then need to calculate p values for each timepoint based on these 4 t statistics.

Also, make sure that you have the right number of parentheses. You were missing some in the formula you had in your spreadsheet.

Once you have made these corrections, you will need to copy it over to the forGenMAPP sheet. Group the data together by timepoint. I.e., put the individual LogFCs, average LogFC, Tstat and P value for each timepoint together.

With these changes, you will be ready for the next step. Please send me an e-mail with a link to the file when you have done them.

Best, — Kdahlquist (talk) 15:46, 26 November 2013 (PST)

At 10:47 AM 11/26/2013, Miles Malefyt wrote: https://xmlpipedb.cs.lmu.edu/biodb/fall2013/index.php/Team_Name#Data_ready_for_GenMAPP

The file is under the section, Data ready for GenMAPP in both .txt and .xls formats