Difference between revisions of "Nstojan1 Week 10"
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Nstojan1-new (talk | contribs) (added purpose and procedure) |
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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. | ||
Revision as of 08:43, 5 April 2024
Rows: 4727 filter greater than 0.05 Media:Screenshots.pptx 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.
- 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.
- Preparing the microarray data file for loading into STEM:
