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  • RES file format interpretation for expression calculation

    Dear all,
    I was trying to analyze the expression data provided in RES formats.
    My specific queries include:

    (1) These absolute values are fold changes (over expression) or what ?
    And are these values compared with those of normal conditions? because I see all the values are above zero (0) only in my data,which give the impression that neither of gene is down regulated !! I mean how can I interpret up regulated and down regulated genes (what cut off values I have to take in this case).
    Because in "sample RES file" at Gene pattern website
    (http://www.broadinstitute.org/cancer...l_aml_test.res)
    there are values in negative also (which I think for down regulated
    genes), but in my data I could not find any negative number.

    (2) For calculating expression data for a particular gene in that
    file, many genes are represented by more than one probe_set ids. So, I
    summed and averaged probeset ids' expression values related to each
    gene. Is it right way to do this?

    (3) Do I have to exclude the values of expression corresponding to M
    and A notation ? Because, my presumption is that only P is significant and should be taken into account for calculating expression data. Am I doing right thing or something is missing ?

    Please suggest the needful.
    Thanking you.

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