[BioC] Question regarding COA plot generated by made4 package

aedin culhane aedin at jimmy.harvard.edu
Wed May 2 16:54:37 CEST 2012

Dear Barbara and Valerie
Thanks for forward this to me Valerie, I had missed it in my Bioc daily 
digest ;-)

The d indicates the scale of the grid squares on the plot

For example

# Load some test data and perform a correspondence analysis
khan.coa<-ord(khan$train, classvec=khan$train.classes, type="coa", 

#This is the same as
plotgenes(khan.coa$ord$li, axis1=1,axis2=2)

#Now lets look at this in more detail.  The correspondence analysis 
results are in $ord, and
# the coordinates for the axis (eigenvectors/principal components) are 
in $ord$li and $ord$co
# where li are the lines (rows) and co are the columns. So if we want to 
examine the genes in more detail, these are in the rows
# so we look at $ord$li

# Note if we scale the data, d changes in the plot to reflect the scale

plotgenes(khan.coa$ord$li, axis1=1,axis2=2)
plotgenes(khan.coa$ord$li*10, axis1=1,axis2=2)
plotgenes(khan.coa$ord$li*100, axis1=1,axis2=2)
plotgenes(khan.coa$ord$li/100, axis1=1,axis2=2)

Hope this helps, please let me know if you have any further questions

> On 04/28/12 21:07, Barbara Shih wrote:
>> Dear all,
>> I am wondering how I should label the quadrants in the coa plot 
>> generated by made4 package (see figure 3, top right in 
>> http://www.bioconductor.org/packages/2.9/bioc/vignettes/made4/inst/doc/introduction.pdf 
>> ). Also, what does the "d" value on the top right hand corner mean?
>> Thank you very much for your help
>> Barbara
>>     [[alternative HTML version deleted]]
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Aedin Culhane
Computational Biology and Functional Genomics Laboratory
Harvard School of Public Health,
Dana-Farber Cancer Institute

web: http://www.hsph.harvard.edu/research/aedin-culhane/
email: aedin at jimmy.harvard.edu
phone: +1 617 632 2468
Fax: +1 617 582 7760

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