Help performing a median polish

[#1]

Hello,

I have cell-based screening data that is showing a row-wise artifact that causes my odd rows (A, C, etc) to be slightly lower in signal than my even rows (B, D etc). While the perfect solution is to mitigate the source of variance in the equipment, I also would like to smooth my data to salvage and better call hits. I have read in a number of papers about Tukey's median polish as being used for screening data to smooth out spatial bias but was unable to determine how to implement this in JMP or if it was already a built-in tool. I know that I could potentially calculate one iteration of this by finding the row/col medians and performing the math, but what makes this tool powerful is the ability to iterate over n-number of cycles until there is negligible change across row and column medians. I was wondering if someone might help me write a script or point me toward a plug-in that could accomplish this task? It would be nice to have a gui window similar to some of the other analysis tools where I could put in my y-variable, my row and column columns, and then any "by" variables. Then also potentially either a box to enter the number of iterations, or some sort of test for residuals so that it can tell itself when to stop iterating and show me the results of each iteration at the end. I am very new to JMP so this is way over my head, but would appreciate any help! I think this could be a powerful addition to the screening analysis tools also, because this has been shown to better smooth data and make hit calling more reliable.  Thanks in advance! 

-Ani 

Link to info about median polish:

https://en.wikipedia.org/wiki/Median_polish

[#2]

I do not believe there is a Median Polish  provided in JMP, however, the JMP interface to Python or R will allow you to access their Median Polish routines.

[#3]

Also, if you're just looking to de-bias alternate rows, you can do so with a few clicks in the GUI. You could also choose Standardized instead of Centered.

 

It does sound like a fun scripting exercise, though. If I were scripting it in JSL, I'd likely follow the steps in this video.

[#4]

... and then maybe replace Col Mean() with Col Median().

To apply the full Median Polish, the data has to be suitable to do so ...
- otherwise a lot of valuable (essential!) information is removed "accidentally".

[#5]

Another approach ...

Oh, I won't mention this time.

[#6]

I'll mention it for you! @hogi's Normalization GUI can also do this.