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Excel File from DNA Microarray Analysis Activity Part 1:
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= Sample Microarray Analysis Vibrio cholerae =
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[[Media:Merrell Compiled Raw Data Vibrio RARL 20151015.xls | Excel Spreadsheet 10/15/2015 edit]]
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== Statistical Analysis ==
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* The data from the Merrell et al. (2002) paper was accessed from [http://www.nature.com/nature/journal/v417/n6889/full/nature00778.html this page] at the Stanford Microarray Database.
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* The Log<sub>2</sub> of R/G Normalized Ratio (Median) has been copied from the raw data files downloaded from the Stanford Microarray Database.
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* Downloaded the [[Media:Merrell_Compiled_Raw_Data_Vibrio.xls | Merrell_Compiled_Raw_Data_Vibrio.xls]] file to my flashdrive.
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** Saved a copy of the file with a different filename that included my initials and the date of download - "Merrell_Compiled_Raw_Data_Vibrio_RARL_20151015.xls"
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Excel File completed on own before class on Thursday, 10/22/2015:
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=== Normalize the log ratios for the set of slides in the experiment ===
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txt. file for GenMAPP:
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To scale and center the data (between chip normalization) I performed the following operations:
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* Inserted a new Worksheet into my Excel file, and named it "scaled_centered".
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* Went back to the "compiled_raw_data" worksheet, Select All and Copy.  Went to my new "scaled_centered" worksheet, clicked on the upper, left-hand cell (cell A1) and Paste.
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* Inserted two rows in between the top row of headers and the first data row.
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* In cell A2, typed "Average" and in cell A3, typed "StdDev".
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* I computed the Average log ratio for each chip (each column of data).  In cell B2, typed the following equation:
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=AVERAGE(B4:B5224)
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: and pressed "Enter".  Excel is computing the average value of the cells specified in the range given inside the parentheses.  Instead of typing the cell designations, I clicked on the beginning cell, scrolled down to the bottom of the worksheet, and shift-click on the ending cell.
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* I then computed the Standard Deviation of the log ratios on each chip (each column of data).  In cell B3, typed the following equation:
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=STDEV(B4:B5224)
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: and pressed "Enter". I copied these two equations (cells B2 and B3) and pasted them into the empty cells in the rest of the columns.  Excel automatically changed the equation to match the cell designations for those columns.
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* Since I computed the average and standard deviation of the log ratios for each chip, I began to actually do the scaling and centering based on these values.
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* I copied the column headings for all of my data columns and then pasted them to the right of the last data column so that I have a second set of headers above blank columns of cells. I edited the names of the columns so that they now read:  A1_scaled_centered, A2_scaled_centered, etc.
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* In cell N4, I typed the following equation:
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=(B4-B$2)/B$3
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: In this case, we want the data in cell B4 to have the average subtracted from it (cell B2) and be divided by the standard deviation (cell B3).  We use the dollar sign symbols in front of the "2" and "3" to tell Excel to always reference that row in the equation, even though we will paste it for the entire column of 5221 genes.  '''''Why is this important?''''' - '''If we were to not include the dollar sign symbols in front of the "2" and "3" then equations that would be copied and pasted in the entire column would not use the values we needed which are found in cell B2 and B3. For instance, without the dollar sign symbols the equation for the next cell would become =(B5-B3/B4), the wrong values are being used for what we want.'''
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* Copied and pasted this equation into the entire column.
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* Copied and pasted the scaling and centering equation for each of the columns of data with the "_scaled_centered" column header. 
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Backtrace:
#0 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(544): DiffEngine->diag()
#1 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(344): DiffEngine->compareSeq()
#2 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(227): DiffEngine->diffLocal()
#3 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(721): DiffEngine->diff()
#4 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(859): Diff->__construct()
#5 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(980): MappedDiff->__construct()
#6 /apps/xmlpipedb/biodb/fall2015/includes/diff/TableDiffFormatter.php(194): WordLevelDiff->__construct()
#7 /apps/xmlpipedb/biodb/fall2015/includes/diff/DiffFormatter.php(140): TableDiffFormatter->changed()
#8 /apps/xmlpipedb/biodb/fall2015/includes/diff/DiffFormatter.php(111): DiffFormatter->block()
#9 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(888): DiffFormatter->format()
#10 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(802): DifferenceEngine->generateTextDiffBody()
#11 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(733): DifferenceEngine->generateContentDiffBody()
#12 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(662): DifferenceEngine->getDiffBody()
#13 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(632): DifferenceEngine->getDiff()
#14 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(453): DifferenceEngine->showDiff()
#15 /apps/xmlpipedb/biodb/fall2015/includes/page/Article.php(795): DifferenceEngine->showDiffPage()
#16 /apps/xmlpipedb/biodb/fall2015/includes/page/Article.php(506): Article->showDiffPage()
#17 /apps/xmlpipedb/biodb/fall2015/includes/actions/ViewAction.php(44): Article->view()
#18 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(395): ViewAction->show()
#19 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(273): MediaWiki->performAction()
#20 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(566): MediaWiki->performRequest()
#21 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(414): MediaWiki->main()
#22 /apps/xmlpipedb/biodb/fall2015/index.php(44): MediaWiki->run()
#23 {main}