BIOL368/F14:Chloe Jones Week 13

Here is the Overton_MicroarrayData_20141119.xlsx used for this analysis of MRSA with Ranalexin.
- Start from the sheet called "SAR_only"
Step. 1 Rename the columns with the item isolated, biological replicate, and dye used. For each array data file there will be 2 columns: signal and background.
Step. 2 Minus the background from the signal for each data file. Then take the answers from each replicate and divide it by its corresponding dye (i.e. Cy5 Ranalexin(B1)/Cy3 MRSA252 (B1)). NOw, the fold change is calculated.
Step 3. Take the log2 of each fold change.

=LOG(number, base)
for example, =LOG(A1,2) takes the log2 of the number in cell A1.

Fix the dye-swapped samples so that the orientation is alwasys ranalexin/control by multiplying the log fold changes of the samples where the control was labeled with Cy5 by negative 1 (-1).

=(-1)*A1 would multiply the number in cell A1 by negative 1.

create a new worksheet. Copy and paste the following columns into the new sheet, ID, index, the log fold changes of the non-dye-swapped samples and the fold changes of the dye-swapped samples that have been flipped. Be sure to use the option, Paste special > paste values instead of a regular copy and paste.
there are probably error messages in certain cells after you have done these calculations. We need to replace all of these with a single space character using the Find/replace option. Record the number of replacements you make.

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