Difference between revisions of "Kzebrows Week 14"
From LMU BioDB 2015
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==Electronic Lab Notebook== | ==Electronic Lab Notebook== | ||
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| + | First, I downloaded the most recent version of the file from the [[OTS Files | OTS Files]] page. I renamed all columns by replacing LR with LogFC. I re-named Sheet 1 "CompiledRawData" and copied all of the data from it and pasted it into Sheet 2, which I re-named "MasterSheet". Next I: | ||
| + | *deleted all ID columns except for column A, which I re-named "ID" | ||
| + | *inserted a column to the left of column B and re-named it "MasterIndex" | ||
| + | *Typed "1" and cell B2 and 2 and Cell B3 | ||
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| + | *3,926 files after deleting "Blank" and "Empty" (3,927 minus 1 header row) | ||
| + | *585 replacements when "Error" was replaced with nothing. | ||
| + | *36 replacements of LR with LogFC | ||
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| + | Following the instructions in [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae Sample Microarray Analysis Vibrio cholerae]: | ||
| + | *I inserted a new worksheet and named it Scaled_Centered | ||
| + | *I copied all data from the MasterSheet and pasted it into cell A1 of the Scaled_Centered sheet | ||
| + | *I inserted two rows in between the top row of headers and first data row. I named cell A2 "Average" and named cell A3 "StdDev". | ||
| + | *In cell C2 I typed =AVERAGE(C4:C3929) and in cell C3 I typed =STDEV(C4:C3929). I pressed enter and copied this equation across the rest of the columns through column AL. | ||
| + | *I then copied the column headings for all data columns and pasted them to the right of the last column. Using the copy/paste tool I renamed each column with "_Scaled_Centered" at the end. | ||
| + | *In cell AM4 I typed =(C4-C$2)/C$3 indicating that I wanted data in cell C4 to have the average subtracted from it and then to divide it by the standard deviation. I used the "$" sign to indicate that I did not want the average and standard deviation values to change even when the equation was pasted for the entire column of genes. | ||
Revision as of 23:39, 1 December 2015
Electronic Lab Notebook
First, I downloaded the most recent version of the file from the OTS Files page. I renamed all columns by replacing LR with LogFC. I re-named Sheet 1 "CompiledRawData" and copied all of the data from it and pasted it into Sheet 2, which I re-named "MasterSheet". Next I:
- deleted all ID columns except for column A, which I re-named "ID"
- inserted a column to the left of column B and re-named it "MasterIndex"
- Typed "1" and cell B2 and 2 and Cell B3
- 3,926 files after deleting "Blank" and "Empty" (3,927 minus 1 header row)
- 585 replacements when "Error" was replaced with nothing.
- 36 replacements of LR with LogFC
Following the instructions in Sample Microarray Analysis Vibrio cholerae:
- I inserted a new worksheet and named it Scaled_Centered
- I copied all data from the MasterSheet and pasted it into cell A1 of the Scaled_Centered sheet
- I inserted two rows in between the top row of headers and first data row. I named cell A2 "Average" and named cell A3 "StdDev".
- In cell C2 I typed =AVERAGE(C4:C3929) and in cell C3 I typed =STDEV(C4:C3929). I pressed enter and copied this equation across the rest of the columns through column AL.
- I then copied the column headings for all data columns and pasted them to the right of the last column. Using the copy/paste tool I renamed each column with "_Scaled_Centered" at the end.
- In cell AM4 I typed =(C4-C$2)/C$3 indicating that I wanted data in cell C4 to have the average subtracted from it and then to divide it by the standard deviation. I used the "$" sign to indicate that I did not want the average and standard deviation values to change even when the equation was pasted for the entire column of genes.
