Talk:Team Name

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

Feeback for Lauren

E-mail sent on 11/26/13 04:14 PM

Hi Lauren,

I have reviewed your spreadsheet and you need to make the following changes:

First, for every new sheet you need to copy over the column with the GeneIDs. This is really important so that you know for sure which data belongs to which ID.

On sheet2 (the one in which you did the scaling and centering), when you copied and pasted the equation for scaling and centering the chips, you repeated one column and thus all the columns to the right of that one are off. Column N is the same as Column O. Column O should have the equation for the data from column C, not column B. All of the columns to the right of column O are shifted by one. You need to go back and fix the equations for all of these. You will then need to repeat the rest of your analysis since you did it with the wrong numbers.

On sheet3 (your statistics sheet), your equations for the TSTAT are off. You are missing one set of parentheses.

Please make these changes, being careful to copy over the gene IDs to each sheet. You will need to redo things starting from the scaling and centering. When you redo the statistics, make sure to check the parentheses on your equation for the TSTAT.

Your final sheet for GenMAPP is not formatted correctly either. Please follow the changes in the protocol. Like I said to Miles, please group the data for each of the timepoints together.

When you have made these changes, please send me the link to your file.

It would be helpful if you gave your filename a more specific title than just "final spreadsheet"--you should include your initials and date at least in the filename to distinguish it from other peoples and other groups.

Best,

— Kdahlquist (talk) 16:14, 26 November 2013 (PST)

At 10:47 AM 11/26/2013, Lauren Magee wrote: hi Dr. Dahlquist, If you could give this file a look over break that would be great! It is located on my team page: https://xmlpipedb.cs.lmu.edu/biodb/fall2013/index.php/Team_Name in the section labeled "Micro Array paper" and it is the final two documents (one is .txt, one is .xls). Thank you and have a great break! -Lauren Magee