Assuming that you have counts per gene, you can use any number of heatmap functions. A quick search of the bioconductor archives will turn up many examples/possibilities. If you are asking about how to get counts per gene and do analyses looking for differential expression, then you might want to give a bit more detail of your experiment.<br>
<br>Sean<br><br><div class="gmail_quote">On Tue, Mar 3, 2009 at 6:43 PM, Carl Yeoman <span dir="ltr"><<a href="mailto:cjyeoman@illinois.edu">cjyeoman@illinois.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<p>Hi,</p>
<p>I was hoping someone might point me in the direction of the
best package (in R) for generating heatmaps from my solexa analysis of a
transcriptome. Quantitative and statistical analysis were performed using
ShortRead.</p>
<p>Carl</p>
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