Laurmagee: Week 13

The following link is to the Sinorhizobium meliloti team page: Team Name

• After downloading all of the files off of the following link last week: [Microarray Downloads], I began compiling the data and computing the log((Cy5 Signal- Cy5 background)/(Cy3 Signal- Cy3 background)) for every replicate (1-3) corresponding with the four different times offered in the experiment (15, 30, 60, 240) when adding 0.7 M sucrose.
• The following files are representing the data for every specific replicate at a specific time. The labeling 700S represents .7M sucrose and the following numbers (1-3) represent the replicate number. Then t(15, 30, 60, 240) represents each time period that was taken.
  • File:700S1-t15.xls
  • File:700S1-t30.xls
  • File:700S1-t60.xls
  • File:700S1-t240.xls
  • File:700S2-t15.xls
  • File:700S2-t30.xls
  • File:700S2-t60.xls
  • File:700S2-t240.xls
  • File:700S3-t15.xls
  • File:700S3-t30.xls
  • File:700S3-t60.xls
  • File:700S3-t240.xls
• These files were created by extracting the Cy5 Signal, Cy5 Background, Cy3 Signal, and Cy3 Background median values and placing them into a new worksheet.
• In the A column is the Cy3 Signal median, B column Cy3 Background median, and the C column is Cy3 Signal-Cy3 Background, which are values found by entering in the following equation into C2: =A2-B2. You can copy and paste this equation into the rest of the column by copying the C2 cell and highlighting it, then scrolling down to the last value and selecting it while pressing the SHIFT key. This will highlight the entire column and you can paste the equation into all of the columns easily by hitting COMMAND and then V.
• In the D column, we will now add Cy5 Signal median, in the E column Cy5 Background median, and finally in column F label Cy5 Signal-Cy5 Background. In the F2 cell, you will enter the equation: =D2-E2. copy and paste this equation into the rest of the F column by using the steps described above for column C.
• Then finally in column G, we will find the value of (Cy5 Signal- Cy5 background)/(Cy3 Signal- Cy3 background) by entering in the following equation into the G2 cell: =C2/F2 and pasting it into the rest of the G column.
• The above steps were repeated twelve times for each of the three replicates and their four time measurements.
• The following file is a compilation of all the Cy5/Cy3 ratios, with the addition of the log of these values: File:Compiled Ratios and Logs.xls
• The A column includes the Gene IDs, and then the B, D, F, H, J, L, N, P, R, T, V, X include the Cy5/Cy3 ratios for each time period and replicant. To find the log of each column, the following equation was entered: =log(B2) into cell C2. Then the equation was copy and pasted in the whole C column. In the subsequent empty columns, the same log equation is inserted, with the appropriate letter representing the column to the left.
• The final data file is: File:Full Raw Data.xls

Laurmagee (talk) 12:35, 21 November 2013 (PST)