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<p class=MsoNormal><span style='color:black'>Two questions:<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p>
<p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='color:black'><span style='mso-list:Ignore'>1)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='color:black'>Is there a package in
R that will allow me to map transcriptional responses (as determined by RNAseq using
Solexa and scaffolded to a complete and annotated genome) to Kegg pathways? If
so what is it/are they? And if there are several which is the best?<o:p></o:p></span></p>
<p class=MsoListParagraph><span style='color:black'><o:p> </o:p></span></p>
<p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='color:black'><span style='mso-list:Ignore'>2)<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='color:black'>This is a question I
asked previously but didn’t get a satisfactory answer:<o:p></o:p></span></p>
<p>I was hoping someone might point me in the direction of a good package (in
R) for generating heatmaps from my prescaffolded (using Novalign with quantitative
and statistical analysis performed using ShortRead; so I already have counts
per gene and information on differential expression between the conditions
tested) solexa analysis of a transcriptome.<o:p></o:p></p>
<p class=MsoNormal><span style='color:black'>I’m aware there may be many
but can someone point me in the direction of one that they have used successfully
and would be compatible. <o:p></o:p></span></p>
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