[BioC] clusterCt {HTqPCR}

[Heidi Dvinge]

> Dear all,
>
> Newbie:
>
> I have done a 384 well plate qPCR and I want to draw a cluster for
> genes (384 genes). How may "make" R to "widen" graphic window for
> clusters?
>
Depends on what graphic system you're using. With e.g. quartz on a mac you
can say:

quartz(width=12)
clusterCt(qPCRraw, type="genes", cex=0.5)

I assume there's something similar for X11. Basically, most devices will
let you set width and height, same as you would do when using pdf() to
write to a file.

What you might want to do, is using the output from clusterCt() to get a
list of the content of the different subclusters.

> c.list <- clusterCt(qPCRraw, type="genes", n.cluster=7)
> sapply(c.list, length)
[1] 68 72 77 12 44 44 65
> c.list[[1]]
  Gene4   Gene6  Gene11  Gene16   Gene4  Gene11  Gene13  Gene16
      4       6      12      17      28      36      38      41
 Gene28  Gene30  Gene32  Gene33  Gene35  Gene38  Gene44  Gene28
     53      55      57      58      60      63      69      77
 Gene30  Gene32  Gene33  Gene35  Gene38  Gene44  Gene51  Gene63
     79      81      82      84      87      93     100     112
 Gene51  Gene63  Gene85  Gene90  Gene85  Gene95  Gene96  Gene99
    124     136     158     163     181     190     191     194
Gene102  Gene96  Gene99 Gene102 Gene110 Gene122 Gene125 Gene126
    197     215     218     221     229     241     244     245
Gene136 Gene143 Gene122 Gene125 Gene126 Gene136 Gene139 Gene143
    255     262     265     268     269     279     282     286
Gene153 Gene154 Gene155 Gene157 Gene159 Gene161 Gene167 Gene153
    296     297     298     300     302     304     310     320
Gene154 Gene155 Gene157 Gene159 Gene161 Gene167 Gene171 Gene181
    321     322     324     326     328     334     338     348
Gene191 Gene171 Gene181 Gene191
    358     362     372     382


HTH
\Heidi

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