Nstojan1 Week 10 - Revision history

Nstojan1-new: added step 2

2024-04-05T15:44:52Z

added step 2

2024-04-05T15:43:03Z

added to procedure

2024-04-05T15:38:31Z

added purpose and procedure

2024-03-21T22:07:02Z

added file

2024-03-21T22:05:53Z

added media

2024-03-21T21:22:11Z

entered row

New page

Rows: 4727 filter greater than 0.05

← Older revision		Revision as of 15:44, 5 April 2024
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	#**If you had #DIV/0! errors, to remove them, open Find/Replace dialog. Search #DIV/0!, but don't put anything in the replace field. Click "Replace all" to remove the errors		#**If you had #DIV/0! errors, to remove them, open Find/Replace dialog. Search #DIV/0!, but don't put anything in the replace field. Click "Replace all" to remove the errors
	#**Save the work. Use Save As to saver the spreadsheet as Text. Click OK to warnings and close the file.		#**Save the work. Use Save As to saver the spreadsheet as Text. Click OK to warnings and close the file.
		+
		+	#*Now download and extract the STEM software. Click here to go to the STEM web site.
		+	#**Click on the download link and download the stem.zip file to your Desktop.
		+	Extract the file by right-clicking on it and selecting "Extract all" from the menu.
		+	This will create a folder called stem.
		+	You now need to download the Gene Ontology and yeast GO annotations and place them in this folder.
		+	Click here to download the file "gene_ontology.obo".
		+	Click here to download the file "gene_association.sgd.gz".
		+	Inside the folder, double-click on the stem.jar to launch the STEM program.

← Older revision		Revision as of 15:43, 5 April 2024
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	#**Filter the data on the B-H corrected value to be > 0.05		#**Filter the data on the B-H corrected value to be > 0.05
	#**Once it has been filtered, select all of the rows (not header row) and delete the row by right clicking and choosing "Delete Row" from the context menu. Undo the filter, this will cluster only the genes with "significant" change in expression and not the noise.		#**Once it has been filtered, select all of the rows (not header row) and delete the row by right clicking and choosing "Delete Row" from the context menu. Undo the filter, this will cluster only the genes with "significant" change in expression and not the noise.
		+	#**Delete all of the columns EXCEPT for the Average Log Fold change columns for each timepoint.
		+	#**Rename the columns with just the time and unites, for example 15m,30m,etc.
		+	#**If you had #DIV/0! errors, to remove them, open Find/Replace dialog. Search #DIV/0!, but don't put anything in the replace field. Click "Replace all" to remove the errors
		+	#**Save the work. Use Save As to saver the spreadsheet as Text. Click OK to warnings and close the file.

← Older revision		Revision as of 15:38, 5 April 2024
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	[[Media:Screenshots.pptx]]		[[Media:Screenshots.pptx]]
	[[Media:Natalija_Stojanovic_File_New.xlsx]]		[[Media:Natalija_Stojanovic_File_New.xlsx]]
		+
		+	Rows: 4727 filter greater than 0.05
		+	[[Media:Screenshots.pptx]]
		+	[[Media:Natalija_Stojanovic_File_New.xlsx]]
		+
		+	*Purpose: The purpose of this assignment is to analyze a DNA microarray dataset that involves clustering and analysis of gene regulation networks using the GRNsight software.
		+
		+	*Procedure:
		+	#*Preparing the microarray data file for loading into STEM:
		+	#**Insert a new worksheet into Excel workbook, and make it dCIN5_stem
		+	#**Select all the data from "dCIN5_ANOVA" worksheet and Paste Special > paste the values into "dCIN5_stem" worksheet.
		+	#**The leftmost column should have a column header "Master Index". Rename it to "Spot". Rename Column B ("ID") to "Gene Symbol" and delete the column named "Standard_Name".
		+	#**Filter the data on the B-H corrected value to be > 0.05
		+	#**Once it has been filtered, select all of the rows (not header row) and delete the row by right clicking and choosing "Delete Row" from the context menu. Undo the filter, this will cluster only the genes with "significant" change in expression and not the noise.

← Older revision		Revision as of 22:07, 21 March 2024
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	Rows: 4727 filter greater than 0.05		Rows: 4727 filter greater than 0.05
	[[Media:Screenshots.pptx]]		[[Media:Screenshots.pptx]]
		+	[[Media:Natalija_Stojanovic_File_New.xlsx]]