Vkuehn Week 13

Week 13 Individual Lab Notebook

From this week on, your Individual Journal Assignment will be to complete your electronic laboratory notebook that records your work on your team's final project.

11/19/13

Understanding the array data:

• data from several independent L. infantum and L. major DNA microarray experiments were compiled and compared
• compared each gene according to the normalized log2 ratio of the Alexa 647/Alexa 555 signal intensities (amastigotes/promastigotes) and to the signal mean intensity of each spot
• Transcriptional analyses of L. infantum promastigote compared to L. infantum intracellular amastigote, and L. major promastigote compared to L. major intracellular amastigote

The full-genome DNA microarray includes one 70mer-oligonucleotide probe for each gene of L. infantum and for each gene of L.major LV39

• Lmj Sample Info: The replicate numbers and sample IDs correspond to our txt files. (22, 24, 25, 28, 30 were dye swaps)

You need to record a narrative that describes all of the methods that you are using in enough detail so that the instructors or your other team members can follow and reproduce your work.

Include links to artifacts you produce (files, images, testing reports, code, etc.)

11/21/13

Scaled and Centered the L. major data and performed statistical analysis

• Working with the data:
  1. Create new worksheet and copy over all the data
  2. Find STDEV and AVG for each column as new rows on top
  3. Create new columns next to the sample columns, label name_SC
  4. Scale and center doing (Value-AVG)/STDEV for each sample
• Inserted new worksheet called Statistics
  1. Added 3 new columns: Avg_Log_FC_A, Avg_Log_FC_B, Avg_Log_FC_C
  2. Delete the other columns and keep only the SC columns. Delete 2 empty rows on top
  3. Compute average log full change for all of the samples ex:(=AVG(B2:E2))
  4. T-test: =AVERAGE(N2:P2)/(STDEV(N2:P2)/(SQRT(# of replicates))
  5. Determine if it is significantly different than zero
  6. Create new column titled P-Value and Calculated the P-value lower than 0.05 (Got 948 values that were significant).
• Created new worksheet titled GenMAPP
  1. copy over the data from Statistics worksheet (using values only)
  2. Select all fold changes and format cells under number tab to 2 decimal places
  3. Do the same for columns R and S
  4. Delete AVG and STDEV rows
  5. Insert "SystemCode" column next to the ID column and input "N" for all rows
  6. Save as tab-delimited text file