in reply to Re^5: Code Critique
in thread Code Critique

Thank you. My second bit of code, which I've alluded to, is what does the more intense processiong of this data. The point of this is to give the data a common format. Once I have that common format, then I'm doing a lot more with it e.g.

- Working out trends (using least squares for now)

- Sorting by date (I added an epoch datafield and sorted from that key as an approach.)

-Exporting it to csv and a graphing tool.

My home's up side down at the moment with my study being repainted, and my PC is needing reconstruction - So I haven't had much time to restructure yet - hopefully I'll have time this weekend. Here's an example of the end output.

http://www.flickr.com/photos/37312673@N05/5059015903/

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Re^7: Code Critique
by Marshall (Canon) on Oct 10, 2010 at 00:05 UTC
    I looked at your graph. Nice. Would be interested in knowing the tool that you used for this graph? Graph is labeled as PSA, perhaps Prostate Specific Antigen?

    Getting off the topic of Perl, but some things to consider for the presentation.. What's normal or not for PSA is based upon prostate size, not some absolute value. Normal tissue produces 0.066 ng/mL/cc of prostate volume. Basically any value above 2.5 is worthy of some investigation as to the cause, perhaps BPH (Benign Prostatic Hyperplasia) etc. Evidence of disease is an exponential growth rate, like 2,4,8,16.

    Plot log(PSA) vs time. The logarithmic plot makes it easier to discern trends and many biological markers exhibit this type of growth. If the log plot is a straight line going upwards and to the right, then the slope of that line determines how fast things are progressing. From the slope of the log line, you can determine the "doubling rate", how long it takes for the tumor to double. That is a key prognostic factor and would help you quantify "getting worse fast".

    If you are writing code that is not-for-profit and can be shared amongst institutions for the general benefit of all, I will help you with this project and perhaps other Monks would also. Send a /msg to me and we'll discuss further off-line.

    I apologize for the non Perl part of this thread. But perhaps the tip about plotting log values instead of a linear plot could be counted as relevant.

      Sorry for gbeing away. Real life intervened. The graphs are done using Visifire. PSA is indeed prostate specific antigen. This tool works for any value though, and is designed to look at biomedical data. As you point out the doubling rate, or just the rate of increase is a massively useful value. By plotting a log rate, it makes the graphs easier for us, but risks making them more difficult for the end user. I was planning to open source all of this as soon as I got it into a fit state for others to understand.