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==August 28th== *TO DO TODAY: **Take log of various factors in R, see if this affects ''lm'' results. **See if any other combinations of factors produce better fits in R. **Implement algorithm to select probes in Perl. *'''R Analysis of Cosmic Data Set''' **Tried taking the log of all factors aside from Tm, checked fit. **Fit is still not very good ***Very low R^2 value ***Checked by plotting in Octave; fit does not match up to data well at all. **Perhaps a different, non-linear, non-logarithmic model is needed? **One issue with the Cosmic Data Set is that there is no data for oligonucleotide bias on the chip. ***Agilent's chips have some inherent bias in what molecules are present and not present. ***This bias was measured for the CES22k set that Dr. Zhang worked on but ''not'' for the Cosmic set. ***This may be causing issues with fitting a curve to the Cosmic set, as this bias cannot be used in the fit. **Came up with some ideas while working from home. ***Perhaps instead of log or linear fit, use a normal distribution type fit? ***Could fit a normal distribution to each factor and try and standardize it; this might result in a better overall fit. ***I am currently looking into how to easily do this in R or Octave; shouldn't be too hard to do a fit this way. **Received data for CES22K set ***A preliminary look at the data in Octave makes it seem that R^2 values will remain very low. ***Confirmed that fit is not that great in Octave. ***However, data for bias is present; this means that this can be factored into the analysis. ***Work on this tomorrow.
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