MAplot: Binning grid too coarse for current (small) bandwidth
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neverstop • 0
@neverstop-7227
Last seen 5.3 years ago

I have 49 samples. I need to compare different normalizations applied to Affymetrix data. A way to do that is by using the function MAplot. The problem is that I get some warnings I don't understand:
> MAplot(Data, plot.method="smoothScatter",cex=0.5,cex.main=0.5)


Attaching package: ‘hgu133plus2cdf’

The following objects are masked from ‘package:hgu133acdf’:

    i2xy, xy2i

Warning messages:
1: In KernSmooth::bkde2D(x, bandwidth = bandwidth, gridsize = nbin,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
2: In KernSmooth::bkde2D(x, bandwidth = bandwidth, gridsize = nbin,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
3: In KernSmooth::bkde2D(x, bandwidth = bandwidth, gridsize = nbin,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
4: In KernSmooth::bkde2D(x, bandwidth = bandwidth, gridsize = nbin,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
5: In KernSmooth::bkde2D(x, bandwidth = bandwidth, gridsize = nbin,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
6: In KernSmooth::bkde2D(x, bandwidth = bandwidth, gridsize = nbin,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
7: In KernSmooth::bkde2D(x, bandwidth = bandwidth, gridsize = nbin,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
8: In KernSmooth::bkde2D(x, bandwidth = bandwidth, gridsize = nbin,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

 

Thank you.


affy affymetrix affymetrics affymetrixchip • 1.4k views
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