Dear

 

 

When using the arrayQualityMetrics package on my Affymetrix data, a full
report (the .html-file) gets generated but I get these warnings:

The directory ### has been created.

KernSmooth 2.23 loaded

Copyright M. P. Wand 1997-2009

(loaded the KernSmooth namespace)

[[1]]

 

NULL

NULL

Warning messages:

1: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :

  Binning grid too coarse for current (small) bandwidth: consider increasing
'gridsize'

2: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :

  Binning grid too coarse for current (small) bandwidth: consider increasing
'gridsize'

3: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :

  Binning grid too coarse for current (small) bandwidth: consider increasing
'gridsize'

4: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :

  Binning grid too coarse for current (small) bandwidth: consider increasing
'gridsize'

5: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :

  Binning grid too coarse for current (small) bandwidth: consider increasing
'gridsize'

6: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :

  Binning grid too coarse for current (small) bandwidth: consider increasing
'gridsize'

 

I use R version 2.9.2. Info about the data:

AffyBatch object

size of arrays=1002x1002 features (8 kb)

cdf=Mouse430_2 (45101 affyids)

number of samples=3

number of genes=45101

annotation=mouse4302

notes=

 

Can I increase the 'gridsize'?

The pdf's created also have very big sizes (e.g. meansd.pdf: 27.402 KB,
spatial.pdf: 139.915 KB), is it possible to create smaller sized graphs?

 

 

Regards

 

Koen Marien

student Bioscience Engineering: Cell and Gene Biotechnology

University of Ghent


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