Dahlquist:Notebook/Nutrigenomics/2009/11/19

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2009-11-19

Stephen

  • Table of Mice in Paper vs. Mice on Disk
Mouse Number Mouse name in paper Mouse name on disk
1 WT (non-transgenic) Wk 12 1_12 wk_WILD.CEL
1 WT (non-transgenic) Wk 17 1_17 wk_WILD.CEL
1 WT (non-transgenic) Wk 24 1_24 wk_WILD.CEL
1 Water fed Wk 12 1_12 wk_TRAMP.CEL
1 Water fed Wk 17 1_17 wk_TRAMP.CEL
1 Water fed Wk 24 1_24 wk_TRAMP.CEL
1 GTC fed Wk 12 1_12 wk_TRAMP_treated.CEL
1 GTC fed Wk 17 1_17 wk_TRAMP_treated.CEL
1 GTC fed Wk 24 (tumor free) 1_24 wk_TRAMP_treat_TumorsFree.CEL
1 GTC fed Wk 24 (tumors) 1_24 wk_TRAMP_treat_Tumors.CEL
2 WT (non-transgenic) Wk 12 2_12 wk_WILD.CEL
2 WT (non-transgenic) Wk 17 2_17 wk_WILD.CEL
2 WT (non-transgenic) Wk 24 2_24 wk_WILD.CEL
2 Water fed Wk 12 2_12 wk_TRAMP.CEL
2 Water fed Wk 17 2_17 wk_TRAMP.CEL
2 Water fed Wk 24 2_24 wk_TRAMP.CEL
2 GTC fed Wk 12 2_12 wk_TRAMP_treated.CEL
2 GTC fed Wk 17 2_17 wk_TRAMP_treated.CEL
2 GTC fed Wk 24 (tumor free) 2_24 wk_TRAMP_treat_TumorsFree.CEL
2 GTC fed Wk 24 (tumors) 2_24 wk_TRAMP_treat_Tumors.CEL
3 WT (non-transgenic) Wk 12 3_12 wk_WILD.CEL
3 WT (non-transgenic) Wk 17 3_17 wk_WILD.CEL
3 WT (non-transgenic) Wk 24 3_24 wk_WILD.CEL
3 Water fed Wk 12 3_12 wk_TRAMP.CEL
3 Water fed Wk 17 3_17 wk_TRAMP.CEL
3 Water fed Wk 24 3_24 wk_TRAMP.CEL
3 GTC fed Wk 12 3_12 wk_TRAMP_treated.CEL
3 GTC fed Wk 17 3_17 wk_TRAMP_treated.CEL
3 GTC fed Wk 24 (tumor free) 3_24 wk_TRAMP_treat_TumorsFree.CEL
3 GTC fed Wk 24 (tumors) 3_24 wk_TRAMP_treat_Tumors.CEL

Dr. Dahlquist

  • Stephen was unable to load his files last week into dChip, so I am going to try and see if I can do it.
  • Opened file <1_12 wk_TRAMP.CEL> with Excel (did not completely load) to check the version number of the Affy chip.
    • Chip verion is MOE430A.1sq
    • Verified that all .CEL files had same chip version
    • noticed that the 18th line of the file did not load properly into Excel and was showing the box tab characters
  • Affy Site for this chip
    • Downloaded <moe430_libraryfile.zip>, shown as Library Files > Mouse Expression Set 430 (zip, 24 MB) on the Affy site.
    • Unzipped with 7-zip. The actual CDF file is found in CD_MOE430\Full\MOE430A\LibFiles\MOE430A.CDF. Copied it and moved it to the higher directory with the data.
  • Launched dChip (Build date: Jul 13 2009)
  • Chose menu item Analysis > Open Group
  • Called group "dChip"
  • Chose file directory with .CEL files
  • Said that suffix of TXT/CHP file was .CEL
  • Under Other information tab, selected MOE430A.CDF file
  • Clicked OK and got the following messages.
  • Data appeared to load correctly and create a .dcp file for each .CEL file.
  • Stephen verified that a "Group" should be all of the chips in the experiment by reading the manual.




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