Dahlquist:Notebook/Nutrigenomics/2010/01/20: Difference between revisions
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[[Media:DChip_array_summary.xls]] | [[Media:DChip_array_summary.xls]] | ||
==Between Chip Normalization== | ===Between Chip Normalization=== | ||
==The steps that were taken in dChip to normalize the samples== | |||
=Opening the data files= | |||
#Open dChip | |||
#Click on Analysis and Open Group | |||
#Clicked OK because the Data location was already saved on dChip | |||
#All of the 32 samples were found and and an array summary file was written | |||
=Normalizing the data= | |||
#Click on Analysis and click Normalize and Model... | |||
#Needed to find the median probe intensity (brightness) | |||
#Went into the excel document dChip_array_summary | |||
#Sorted the 32 samples to find the median, median intensity sample | |||
#The median sample was 1_12wk_TRAMP with a median intensity of 184 | |||
#Clicked OK | |||
#After each of the samples were normalized and the image was created I clicked on OK to continue normalizing the subsequent samples | |||
#Uploaded the completed files to OpenWetWare | |||
==GenMAPP on Human PCa Model== | ==GenMAPP on Human PCa Model== | ||
#Opened GenMAPP 2.1 | |||
#Checked to make sure that the human gene database was selected (data - gene database) | |||
#Clicked on tools in GenMAPP and clicked on MAPPFinder 2.0 and clicked on Calculate New Results | |||
#Clicked to Find File and selected the file for prostate cancer Hs_ED_ProstateCancer_20060130.gex | |||
#Clicked OK | |||
#Clicked on the boxes for Gene Ontology, Calculate P-value, and I chose the color set Hormone vs Primary and saved the file to my folder on my desktop | |||
#Selected increased AND decreased under the criteria | |||
#Clicked Run MAPPFinder | |||
#Going to follow the same procedure for the other 3 color sets, saving them all on the desktop | |||
Revision as of 11:04, 27 January 2010
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1/20/10
Between Chip NormalizationThe steps that were taken in dChip to normalize the samplesOpening the data files
Normalizing the data
GenMAPP on Human PCa Model
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