information file

[greenhand]

Dear Cheng,

  Thanks for making this neat program. I am using dchip 64 version.

  I am analyzing Mouse Gene 1.0 st array data.  I have downloaded the "MoGene-1_0-st-v1.na33.1.mm9.probeset.csv" and old " Gene Ontology (GO) structure files: function.ontology, process.ontology, component.ontology " (I dont know where to find the new files).   I tried to "Tools/make information file" as described http://www.hsph.harvard.edu/cli/complab/dchip/gene_info_file.htm   However, there's an error message everytime I load CSV file "reading file 'c:\....csv' failed or this is not a NEtAffx Annotation or Ortholog CSV file."   the output is this
{Make dChip information file
  Reading Gene ontology file 'C:\microarray\2010-05-11\function.ontology'...
    Found 8780 Gene Ontology terms
  Reading Gene ontology file 'C:\microarray\2010-05-11\component.ontology'...
    Found 2197 Gene Ontology terms
  Reading Gene ontology file 'C:\microarray\2010-05-11\process.ontology'...
    Found 14785 Gene Ontology terms

  Writing file 'C:\microarray\2010-05-11\mousetestinfo.xls' failed; probably it's opened by Excel

Finished}

Then I found "https://sites.google.com/site/dchipsoft/probe-level-analysis/exon-array-data-analysis/gene-st-array/information-file-for-gene-st-arrays "

I used "Use the Python program" generated a 'gene information file' from the csv file.  Then I read my CEL data. on "Open group/other information' I had "MoGene-1_0-st-v1.r3.cdf" CDF file, and "information files" I had the one I just made from Python.  

The data seems read fine, but all Call %P are 0 (I also dont know what are Call %P).  Also under "Tools/gene function enrichment",  "Tools/Gene list by Keywords" were both greyed out.  I exported the expression value, and it didnot have GO information. (it had "probe set, gene, Accession, and gene-expression-data). 

I dont know how to cluster the "filter genes" by Functional group.  Sorry for so many questions and the help on the dchip doesn't work.
Thanks for your program.

Best,

Lee

[greenhand]

Dear Cheng,
  One more question, can dChip export the original expression data with annotation or it has to normalize it first before exportation?
Thanks!
Lee