Mercurial > repos > vladimir-daric > ebio_deseq

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		<h1>DESeq analyse results</h1>
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					Total read counts for each sample : <br />
					<img border="0" src="DESeq_out_TotSamplePlot.png" width="50%" height="50%"/>
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					Proportion of null counts for each condition : <br />
					<img border="0" src="DESeq_out_NullCondPlot.png" width="25%" height="50%"/><br />
					<font color="red"> For the next graphs and calculations, all null counts are removed from data.</font> <br /><br />
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					<a href="http://en.wikipedia.org/wiki/Violin_plot">Violinplot</a> of raw counts for each sample : <br />
					<img border="0" src="DESeq_out_RawViolin.png" width="50%" height="50%"/><br />
					<font color="red"> For the next graphs and calculations, data are normalized.</font> <br /><br />
				</li>
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					<a href="http://en.wikipedia.org/wiki/Violin_plot">ViolinPlot</a> of normalized counts for each sample : <br />
					<img border="0" src="DESeq_out_NormViolin.png" width="50%" height="50%"/>
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					Heatmap of euclidean distances between samples : <br/> <a href="http://bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf#subsection.7.2"> (See DESeq manual, Heatmap of the sample-to-sample distances, figure 16) </a><br/>
					<img border="0" src="DESeq_out_HeatDistPlot.png" width="50%" height="50%"/>
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					Heatmap of count data of the 30 most highly expressed genes :<br /> <a href="http://bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf#subsection.7.1"> (See DESeq manual, Heatmap of the count table, figure 15 left) </a><br />
					<img border="0" src="DESeq_out_HeatCountPlot.png" width="50%" height="50%"/>
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					Distribution of p-values : <br /> (graph shows adjusted p-values when biological replicates are available, raw p-values otherwise)<br />
					<img border="0" src="DESeq_out_histPval.png" width="50%" height="50%"/>
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					Control plot of dispersion estimates : <br/> <a href="http://bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf#section.4">(See DESeq manual)</a><br/>
					<img border="0" src="DESeq_out_EstDispPlot.png" width="50%" height="50%"/><br />
					Red line : regression over all data. <br /><br />
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					MAplot showing normalised mean versus log2 (fold change) for condition two versus condition one : <br /> <a href="http://bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf#section.3">(See DESeq manual)</a> <br />
					<img border="0" src="DESeq_out_MAplot.png" width="50%" height="50%"/><br />
					Red line indicates FoldChange = 1. <br />
					Red points represent genes with an adjusted p-value below the p-value threshold. <br />
					Triangles : infinite fold changes.<br/> <br/>
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					Enriched <a href="http://en.wikipedia.org/wiki/Volcano_plot_%28statistics%29">volcano plot</a> showing differentially expressed genes satisfying p-value and foldchange thresholds provided : <br /> Upper and right panels show, respectively, the projection of log fold change density and the log p-value density. <br />
					<img border="0" src="DESeq_out_volcanoplot.png" width="50%" height="50%"/><br />
					Red points : genes with p-value lower than the p-value threshold provided and foldchange greater than the absolute value of the foldchange threshold provided. Fold change of +Inf and -Inf are plotted on either side of volcano plot.<br /><br />
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					Complete quantitative results :
					<a href="DESeq_out_complete.csv">DESeq_out_complete.csv</a>
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					Results for significantly over-expressed genes :
					<a href="DESeq_out_up_genes.csv">DESeq_out_up_genes.csv</a>
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					Results for significantly sub-expressed genes :
					<a href="DESeq_out_down_genes.csv">DESeq_out_down_genes.csv</a>
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author	vladimir-daric
date	Fri, 25 Apr 2014 05:05:39 -0400
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