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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.
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.