<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Wolfgang<div><br></div><div>I am attaching the plots with highlighted DEG tags before and after 3 different normalization procedures, using all samples. In the second figure., I include the plots for the 3 patients separately before and after TMM normalization</div><div>It looks like the normalization for patient 2 is bad. any idea how I can solve this?</div><div><br></div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; color: rgb(179, 17, 0); font-size: 10px; "><span style="color: #000000">pdf</span><span style="color: #00169a">(</span>'Normalization Plots.pdf'<span style="color: #00169a">,</span><span style="color: #000000">height</span><span style="color: #00169a">=</span><span style="color: #005218">10</span><span style="color: #00169a">,</span><span style="color: #000000">width</span><span style="color: #00169a">=</span><span style="color: #005218">10</span><span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">layout<span style="color: #00169a">(</span>matrix<span style="color: #00169a">(</span><span style="color: #005218">1</span><span style="color: #00169a">:</span><span style="color: #005218">4</span><span style="color: #00169a">,</span><span style="color: #005218">2</span><span style="color: #00169a">,</span><span style="color: #005218">2</span><span style="color: #00169a">,</span>byrow<span style="color: #00169a">=</span><span style="color: #c68800">TRUE</span><span style="color: #00169a">))</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">a<span style="color: #00169a"><-</span>plotSmear<span style="color: #00169a">(</span>PScounts<span style="color: #00169a">, </span>panel.first<span style="color: #00169a">=</span>grid<span style="color: #00169a">(),</span>smooth.scatter<span style="color: #00169a">=</span><span style="color: #c68800">FALSE</span><span style="color: #00169a">,</span>main<span style="color: #00169a">=</span><span style="color: #b31100">'before normalization'</span><span style="color: #00169a">,</span><span style="font: normal normal normal 13px/normal Courier; font-size: 9px; ">de.tags</span><span style="font: normal normal normal 13px/normal Courier; color: rgb(0, 22, 154); font-size: 9px; ">=</span>deg.tgw<span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">ma.plot<span style="color: #00169a">(</span>a<span style="color: #00169a">$</span>A<span style="color: #00169a">,</span>a<span style="color: #00169a">$</span>M<span style="color: #00169a">,</span>plot.method<span style="color: #00169a">=</span><span style="color: #b31100">'add'</span><span style="color: #00169a">,</span>cex<span style="color: #00169a">=</span><span style="color: #005218">0</span><span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">b<span style="color: #00169a"><-</span>plotSmear<span style="color: #00169a">(</span>d.PS<span style="color: #00169a">, </span>panel.first<span style="color: #00169a">=</span>grid<span style="color: #00169a">(),</span>smooth.scatter<span style="color: #00169a">=</span><span style="color: #c68800">FALSE</span><span style="color: #00169a">,</span>main<span style="color: #00169a">=</span><span style="color: #b31100">'after TMM'</span><span style="color: #00169a">,</span><span style="font: normal normal normal 13px/normal Courier; font-size: 9px; ">de.tags</span><span style="font: normal normal normal 13px/normal Courier; color: rgb(0, 22, 154); font-size: 9px; ">=</span>deg.tgw<span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">ma.plot<span style="color: #00169a">(</span>b<span style="color: #00169a">$</span>A<span style="color: #00169a">,</span>b<span style="color: #00169a">$</span>M<span style="color: #00169a">,</span>plot.method<span style="color: #00169a">=</span><span style="color: #b31100">'add'</span><span style="color: #00169a">,</span>cex<span style="color: #00169a">=</span><span style="color: #005218">0</span><span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">rm<span style="color: #00169a">(</span>b<span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">b<span style="color: #00169a"><-</span>plotSmear<span style="color: #00169a">(</span>d.PS.2<span style="color: #00169a">, </span>panel.first<span style="color: #00169a">=</span>grid<span style="color: #00169a">(),</span>smooth.scatter<span style="color: #00169a">=</span><span style="color: #c68800">FALSE</span><span style="color: #00169a">,</span>main<span style="color: #00169a">=</span><span style="color: #b31100">'after RLE'</span><span style="color: #00169a">,</span><span style="font: normal normal normal 13px/normal Courier; font-size: 9px; ">de.tags</span><span style="font: normal normal normal 13px/normal Courier; color: rgb(0, 22, 154); font-size: 9px; ">=</span>deg.tgw<span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">ma.plot<span style="color: #00169a">(</span>b<span style="color: #00169a">$</span>A<span style="color: #00169a">,</span>b<span style="color: #00169a">$</span>M<span style="color: #00169a">,</span>plot.method<span style="color: #00169a">=</span><span style="color: #b31100">'add'</span><span style="color: #00169a">,</span>cex<span style="color: #00169a">=</span><span style="color: #005218">0</span><span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">rm<span style="color: #00169a">(</span>b<span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">b<span style="color: #00169a"><-</span>plotSmear<span style="color: #00169a">(</span>d.PS.3<span style="color: #00169a">, </span>panel.first<span style="color: #00169a">=</span>grid<span style="color: #00169a">(),</span>smooth.scatter<span style="color: #00169a">=</span><span style="color: #c68800">FALSE</span><span style="color: #00169a">,</span>main<span style="color: #00169a">=</span><span style="color: #b31100">'after quantile'</span><span style="color: #00169a">,</span><span style="font: normal normal normal 13px/normal Courier; font-size: 9px; ">de.tags</span><span style="font: normal normal normal 13px/normal Courier; color: rgb(0, 22, 154); font-size: 9px; ">=</span>deg.tgw<span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">ma.plot<span style="color: #00169a">(</span>b<span style="color: #00169a">$</span>A<span style="color: #00169a">,</span>b<span style="color: #00169a">$</span>M<span style="color: #00169a">,</span>plot.method<span style="color: #00169a">=</span><span style="color: #b31100">'add'</span><span style="color: #00169a">,</span>cex<span style="color: #00169a">=</span><span style="color: #005218">0</span><span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">rm<span style="color: #00169a">(</span>b<span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">dev.off<span style="color: #00169a">()</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; color: rgb(0, 22, 154); min-height: 19px; font-size: 10px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; color: rgb(179, 17, 0); font-size: 10px; "><span style="color: #000000">pdf</span><span style="color: #00169a">(</span>'Normalization Plots TMM by pairs.pdf'<span style="color: #00169a">,</span><span style="color: #000000">height</span><span style="color: #00169a">=</span><span style="color: #005218">10</span><span style="color: #00169a">,</span><span style="color: #000000">width</span><span style="color: #00169a">=</span><span style="color: #005218">14</span><span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">layout<span style="color: #00169a">(</span>matrix<span style="color: #00169a">(</span><span style="color: #005218">1</span><span style="color: #00169a">:</span><span style="color: #005218">6</span><span style="color: #00169a">,</span><span style="color: #005218">2</span><span style="color: #00169a">,</span><span style="color: #005218">3</span><span style="color: #00169a">,</span>byrow<span style="color: #00169a">=</span><span style="color: #c68800">TRUE</span><span style="color: #00169a">))</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">a<span style="color: #00169a"><-</span>plotSmear<span style="color: #00169a">(</span>PScounts<span style="color: #00169a">[,</span>c<span style="color: #00169a">(</span><span style="color: #005218">1</span><span style="color: #00169a">,</span><span style="color: #005218">4</span><span style="color: #00169a">)], </span>panel.first<span style="color: #00169a">=</span>grid<span style="color: #00169a">(),</span>smooth.scatter<span style="color: #00169a">=</span><span style="color: #c68800">FALSE</span><span style="color: #00169a">,</span>main<span style="color: #00169a">=</span><span style="color: #b31100">'Patient1 before'</span><span style="color: #00169a">, </span><span style="font: normal normal normal 13px/normal Courier; font-size: 9px; ">de.tags</span><span style="font: normal normal normal 13px/normal Courier; color: rgb(0, 22, 154); font-size: 9px; ">=</span>deg.tgw<span style="color: #00169a">, </span>ylim<span style="color: #00169a">=</span>c<span style="color: #00169a">(-</span><span style="color: #005218">10</span><span style="color: #00169a">,</span><span style="color: #005218">10</span><span style="color: #00169a">))</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">ma.plot<span style="color: #00169a">(</span>a<span style="color: #00169a">$</span>A<span style="color: #00169a">,</span>a<span style="color: #00169a">$</span>M<span style="color: #00169a">,</span>plot.method<span style="color: #00169a">=</span><span style="color: #b31100">'add'</span><span style="color: #00169a">,</span>cex<span style="color: #00169a">=</span><span style="color: #005218">0</span><span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">rm<span style="color: #00169a">(</span>a<span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">a<span style="color: #00169a"><-</span>plotSmear<span style="color: #00169a">(</span>PScounts<span style="color: #00169a">[,</span>c<span style="color: #00169a">(</span><span style="color: #005218">2</span><span style="color: #00169a">,</span><span style="color: #005218">5</span><span style="color: #00169a">)], </span>panel.first<span style="color: #00169a">=</span>grid<span style="color: #00169a">(),</span>smooth.scatter<span style="color: #00169a">=</span><span style="color: #c68800">FALSE</span><span style="color: #00169a">,</span>main<span style="color: #00169a">=</span><span style="color: #b31100">'Patient2 before'</span><span style="color: #00169a">, </span><span style="font: normal normal normal 13px/normal Courier; font-size: 9px; ">de.tags</span><span style="font: normal normal normal 13px/normal Courier; color: rgb(0, 22, 154); font-size: 9px; ">=</span>deg.tgw<span style="color: #00169a">, </span>ylim<span style="color: #00169a">=</span>c<span style="color: #00169a">(-</span><span style="color: #005218">10</span><span style="color: #00169a">,</span><span style="color: #005218">10</span><span style="color: #00169a">))</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">ma.plot<span style="color: #00169a">(</span>a<span style="color: #00169a">$</span>A<span style="color: #00169a">,</span>a<span style="color: #00169a">$</span>M<span style="color: #00169a">,</span>plot.method<span style="color: #00169a">=</span><span style="color: #b31100">'add'</span><span style="color: #00169a">,</span>cex<span style="color: #00169a">=</span><span style="color: #005218">0</span><span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">rm<span style="color: #00169a">(</span>a<span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">a<span style="color: #00169a"><-</span>plotSmear<span style="color: #00169a">(</span>PScounts<span style="color: #00169a">[,</span>c<span style="color: #00169a">(</span><span style="color: #005218">3</span><span style="color: #00169a">,</span><span style="color: #005218">6</span><span style="color: #00169a">)], </span>panel.first<span style="color: #00169a">=</span>grid<span style="color: #00169a">(),</span>smooth.scatter<span style="color: #00169a">=</span><span style="color: #c68800">FALSE</span><span style="color: #00169a">,</span>main<span style="color: #00169a">=</span><span style="color: #b31100">'Patient3 before'</span><span style="color: #00169a">, </span><span style="font: normal normal normal 13px/normal Courier; font-size: 9px; ">de.tags</span><span style="font: normal normal normal 13px/normal Courier; color: rgb(0, 22, 154); font-size: 9px; ">=</span>deg.tgw<span style="color: #00169a">, </span>ylim<span style="color: #00169a">=</span>c<span style="color: #00169a">(-</span><span style="color: #005218">10</span><span style="color: #00169a">,</span><span style="color: #005218">10</span><span style="color: #00169a">))</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">ma.plot<span style="color: #00169a">(</span>a<span style="color: #00169a">$</span>A<span style="color: #00169a">,</span>a<span style="color: #00169a">$</span>M<span style="color: #00169a">,</span>plot.method<span style="color: #00169a">=</span><span style="color: #b31100">'add'</span><span style="color: #00169a">,</span>cex<span style="color: #00169a">=</span><span style="color: #005218">0</span><span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">rm<span style="color: #00169a">(</span>a<span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">b<span style="color: #00169a"><-</span>plotSmear<span style="color: #00169a">(</span>d.PS<span style="color: #00169a">[,</span>c<span style="color: #00169a">(</span><span style="color: #005218">1</span><span style="color: #00169a">,</span><span style="color: #005218">4</span><span style="color: #00169a">)], </span>panel.first<span style="color: #00169a">=</span>grid<span style="color: #00169a">(),</span>smooth.scatter<span style="color: #00169a">=</span><span style="color: #c68800">FALSE</span><span style="color: #00169a">,</span>main<span style="color: #00169a">=</span><span style="color: #b31100">'Patient1 after'</span><span style="color: #00169a">, </span><span style="font: normal normal normal 13px/normal Courier; font-size: 9px; ">de.tags</span><span style="font: normal normal normal 13px/normal Courier; color: rgb(0, 22, 154); font-size: 9px; ">=</span>deg.tgw<span style="color: #00169a">, </span>ylim<span style="color: #00169a">=</span>c<span style="color: #00169a">(-</span><span style="color: #005218">10</span><span style="color: #00169a">,</span><span style="color: #005218">10</span><span style="color: #00169a">))</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">ma.plot<span style="color: #00169a">(</span>b<span style="color: #00169a">$</span>A<span style="color: #00169a">,</span>b<span style="color: #00169a">$</span>M<span style="color: #00169a">,</span>plot.method<span style="color: #00169a">=</span><span style="color: #b31100">'add'</span><span style="color: #00169a">,</span>cex<span style="color: #00169a">=</span><span style="color: #005218">0</span><span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">rm<span style="color: #00169a">(</span>b<span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">b<span style="color: #00169a"><-</span>plotSmear<span style="color: #00169a">(</span>d.PS<span style="color: #00169a">[,</span>c<span style="color: #00169a">(</span><span style="color: #005218">2</span><span style="color: #00169a">,</span><span style="color: #005218">5</span><span style="color: #00169a">)], </span>panel.first<span style="color: #00169a">=</span>grid<span style="color: #00169a">(),</span>smooth.scatter<span style="color: #00169a">=</span><span style="color: #c68800">FALSE</span><span style="color: #00169a">,</span>main<span style="color: #00169a">=</span><span style="color: #b31100">'Patient2 after'</span><span style="color: #00169a">, </span><span style="font: normal normal normal 13px/normal Courier; font-size: 9px; ">de.tags</span><span style="font: normal normal normal 13px/normal Courier; color: rgb(0, 22, 154); font-size: 9px; ">=</span>deg.tgw<span style="color: #00169a">, </span>ylim<span style="color: #00169a">=</span>c<span style="color: #00169a">(-</span><span style="color: #005218">10</span><span style="color: #00169a">,</span><span style="color: #005218">10</span><span style="color: #00169a">))</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">ma.plot<span style="color: #00169a">(</span>b<span style="color: #00169a">$</span>A<span style="color: #00169a">,</span>b<span style="color: #00169a">$</span>M<span style="color: #00169a">,</span>plot.method<span style="color: #00169a">=</span><span style="color: #b31100">'add'</span><span style="color: #00169a">,</span>cex<span style="color: #00169a">=</span><span style="color: #005218">0</span><span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">rm<span style="color: #00169a">(</span>b<span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">b<span style="color: #00169a"><-</span>plotSmear<span style="color: #00169a">(</span>d.PS<span style="color: #00169a">[,</span>c<span style="color: #00169a">(</span><span style="color: #005218">3</span><span style="color: #00169a">,</span><span style="color: #005218">6</span><span style="color: #00169a">)], </span>panel.first<span style="color: #00169a">=</span>grid<span style="color: #00169a">(),</span>smooth.scatter<span style="color: #00169a">=</span><span style="color: #c68800">FALSE</span><span style="color: #00169a">,</span>main<span style="color: #00169a">=</span><span style="color: #b31100">'Patient3 after'</span><span style="color: #00169a">, </span><span style="font: normal normal normal 13px/normal Courier; font-size: 9px; ">de.tags</span><span style="font: normal normal normal 13px/normal Courier; color: rgb(0, 22, 154); font-size: 9px; ">=</span>deg.tgw<span style="color: #00169a">, </span>ylim<span style="color: #00169a">=</span>c<span style="color: #00169a">(-</span><span style="color: #005218">10</span><span style="color: #00169a">,</span><span style="color: #005218">10</span><span style="color: #00169a">))</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">ma.plot<span style="color: #00169a">(</span>b<span style="color: #00169a">$</span>A<span style="color: #00169a">,</span>b<span style="color: #00169a">$</span>M<span style="color: #00169a">,</span>plot.method<span style="color: #00169a">=</span><span style="color: #b31100">'add'</span><span style="color: #00169a">,</span>cex<span style="color: #00169a">=</span><span style="color: #005218">0</span><span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">rm<span style="color: #00169a">(</span>b<span style="color: #00169a">)</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal Monaco; font-size: 10px; ">dev.off<span style="color: #00169a">()</span></div><div><font class="Apple-style-span" color="#00169A" face="Monaco" size="4"><span class="Apple-style-span" style="font-size: 14px;"><br></span></font></div></div><div><br></div><div>On a completely unrelated note, I had saw the video already, hilarious</div><div> It's a pilot to see if we want to move to this technology right now, so it's difficult to convince my bio-collaborator to go beyond 3 right now. So far, some important genes that we do not find in affy arrays because low intensity, also came with zero counts here, even though we used 80bp. And it's great for me to get familiar with teh analysis issues, as ou can see...</div><div><br></div><div><img height="240" width="244" apple-width="yes" apple-height="yes" src="cid:A2A6C541-41A0-4445-B676-0214BB9FCF4A"><img height="224" width="324" apple-width="yes" apple-height="yes" src="cid:E7596746-1AD1-4C13-BDFC-13E06B797A2B"></div><div>Mayte Suarez-Farinas</div><div><div apple-content-edited="true"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>Research Associate, The Rockefeller University</div><div>Biostatistician, The Rockefeller University Hospital</div><div>1230 York Ave, Box 178,</div><div>New York, NY, 10065</div><div>+1(212) 327-8213</div></div><div><br></div></div></div></div><br class="Apple-interchange-newline"> </div><br><div><div>On Nov 24, 2010, at 7:50 PM, <a href="mailto:bioc-sig-sequencing-request@r-project.org">bioc-sig-sequencing-request@r-project.org</a> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><br>Dear Mayte<br><br>How do these plots look like when you make them separately for each<br>subject? (In addition, you could colour the dots according to whether<br>the differential expression analysis for the overall dataset calls them<br>'significant').<br><br>Also, if you compute the M values for each patient separately, how does<br>the pairs plot (scatterplot matrix) look like?<br><br>On a completely unrelated note, I recently saw a movie about studies<br>with 3 patients:<span class="Apple-converted-space"> </span><a href="http://www.xtranormal.com/watch/6878253">http://www.xtranormal.com/watch/6878253</a><br><br> Best wishes<br> Wolfgang</blockquote></div><br></div></body></html>