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Not a real issue, but rather I just don't understand how to read the testCV function results. Help? #39
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I had this question too so I'm answering even though it's from a while ago Cytonorm uses different splines for each cluster to normalize. |
A (somewhat) related question regarding the testCV function graphical results. I don't understand what I'm looking at, quite frankly.
I run it as such:
cvs <- CytoNorm:testCV(fsom, cluster_values = c(a, b), plot = true, verbose = true) where a is (I assume) the start cluster number, and b is the end cluster number (from a ridiculously low value of 3 to an equally ridiculously high value of 20). It generates two plots, and I'm not sure I understand what they are telling me.
On the first plot, the top part shows what looks like downward moving "stairs", from 3 to 20 in length (from left to right); they are all shades of blue. If I assume this means that there are no batch effects causing issues with my data, then I really don't understand the following part of the plot! This is followed on the same plot by a box of varying shades of yellow (and red) to blue with values (a 20x20 grid) and with "Original clustering" on the right. I'm not sure how to read this. I understand that anything over 1.5 (or between 1 and 1.5) shows batch effects causing potential issues?
The second plot is an 11 x 20 grid, again with numbers (there are 11 technical controls in the group tested), 20 across and 11 deep. What does this plot mean? Again, the colors range from blue to red...
A third plot is simply a combination of the two previous plots, all on the same page. This one can obviously be read if I knew how to read the other ones. I hate to be ignorant, but... :) I'm having to explain this to others at work and my google-fu appears weak. I would be grateful for any help anyone could give.
Thanks,
Diana
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