Dahlquist:Notebook/Nutrigenomics/2009/11/12

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11/12/2009

  1. Downloaded dChip software from the internet
  2. Found the Affymetrix chip that was used in the study (GeneChip Mouse Genome 430 2.0 arrays)in .cdf form
  3. Attempted to convert the data received from McCarthy et al into dChip compatible data (.dcp)
  4. Wasn't finding the files, so went into original folders from the paper and checked and unchecked "Read Only" and clicked "Apply"
  5. Went back into dChip tried to convert all of the .CEL files into .dcp files
  6. The files still did not convert into the .dcp file
  7. The following error message appeared upon trying to convert into the .dcp format
  8. Error Message
 Treat this array type as 'Expression'
 Read in existing binary CDF file C:\Documents and Settings\sspeiche\Desktop\TrampData\Mouse430_2.cdf.bin (file format 4)...

 Search and extract 'CEL' probe data files of chip type 'Mouse430_2' in 'C:\Documents and Settings\sspeiche\Desktop\TrampData'...

 Found C:\Documents and Settings\sspeiche\Desktop\TrampData\1_12 wk_TRAMP.CEL
   Accessing '1_12 wk_TRAMP.dcp' (file format 4) 
 Found C:\Documents and Settings\sspeiche\Desktop\TrampData\1_12 wk_TRAMP_treated.CEL
   Have the same time tag [] as 'C:\Documents and Settings\sspeiche\Desktop\TrampData\1_12 wk_TRAMP.CEL', ignored; or uncheck 'Open group/options/Check CEL file time tag'
 Found C:\Documents and Settings\sspeiche\Desktop\TrampData\1_12 wk_WILD.CEL
   Have the same time tag [] as 'C:\Documents and Settings\sspeiche\Desktop\TrampData\1_12 wk_TRAMP.CEL', ignored; or uncheck 'Open group/options/Check CEL file time tag'
 Found C:\Documents and Settings\sspeiche\Desktop\TrampData\1_17 wk_TRAMP.CEL
   Have the same time tag [] as 'C:\Documents and Settings\sspeiche\Desktop\TrampData\1_12 wk_TRAMP.CEL', ignored; or uncheck 'Open group/options/Check CEL file time tag'
 Found C:\Documents and Settings\sspeiche\Desktop\TrampData\1_17 wk_TRAMP_treated.CEL
   Have the same time tag [] as 'C:\Documents and Settings\sspeiche\Desktop\TrampData\1_12 wk_TRAMP.CEL', ignored; or uncheck 'Open group/options/Check CEL file time tag'




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