Dahlquist:Notebook/Nutrigenomics/2010/01/20

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 * style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]] Nutrigenomics
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 * style="background-color: #F2F2F2" align="center"|  |Main project page


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1/20/10
[[Media:DChip_array_summary.xls]]
 * The main goals for today-do the between chip normalization and run GenMAPP on the human prostate cancer model

The steps that were taken in dChip to normalize the samples
=Opening the data files= =Normalizing the data=
 * 1) Open dChip
 * 2) Click on Analysis and Open Group
 * 3) Clicked OK because the Data location was already saved on dChip
 * 4) All of the 32 samples were found and and an array summary file was written
 * 1) Click on Analysis and click Normalize and Model...
 * 2) Needed to find the median probe intensity (brightness)
 * 3) Went into the excel document dChip_array_summary
 * 4) Sorted the 32 samples to find the median, median intensity sample
 * 5) The median sample was 1_12wk_TRAMP with a median intensity of 184
 * 6) Clicked OK
 * 7) After each of the samples were normalized and the image was created I clicked on OK to continue normalizing the subsequent samples
 * 8) Uploaded the completed files to OpenWetWare

GenMAPP on Human PCa Model

 * 1) Opened GenMAPP 2.1
 * 2) Checked to make sure that the human gene database was selected (data - gene database)
 * 3) Clicked on tools in GenMAPP and clicked on MAPPFinder 2.0 and clicked on Calculate New Results
 * 4) Clicked to Find File and selected the file for prostate cancer Hs_ED_ProstateCancer_20060130.gex
 * 5) Clicked OK
 * 6) 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
 * 7) Selected increased AND decreased under the criteria
 * 8) Clicked Run MAPPFinder
 * 9) Going to follow the same procedure for the other 3 color sets, saving them all on the desktop


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