Dahlquist:Notebook/Nutrigenomics/2009/11/19

Nutrigenomics

2009-11-19

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

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.