583e30e3cbfc3c95eb94696d51c8979493caa9a3 galt Mon May 20 23:49:34 2019 -0700 html pages fixed for problems found with htmlCheck validate and strictTagNestCheck diff --git src/hg/near/hgNear/hgNearData/affyExonTissuesGs.html src/hg/near/hgNear/hgNearData/affyExonTissuesGs.html index fe53bb4..daa4394 100644 --- src/hg/near/hgNear/hgNearData/affyExonTissuesGs.html +++ src/hg/near/hgNear/hgNearData/affyExonTissuesGs.html @@ -15,46 +15,46 @@ Black indicates that a gene is neither over- nor under-expressed in the tissue. Uncolored boxes (white on most browsers) represent missing data. </P> <H3>Column Configuration</H3> <P> Several column configuration options are available on the Configuration page, which can be accessed via the <em>configure</em> button in the top menu. <UL> <LI> <B>Absolute expression values:</B> The display can be configured to show absolute expression values rather than ratio values. To toggle the display, select the <em>absolute</em> option from the <em>values</em> pulldown menu. Absolute expression values are shown in shades of gray, with higher expression levels shown in lighter shades. As with ratio values, absolute values are colored on a logarithmic -scale. +scale.</LI> <LI> <B>Color scheme:</B> Color-blind users can switch the coloring scheme from red/green to yellow/blue via the <em>Expression ratio colors</em> pulldown -menu at the top of the Configuration page. +menu at the top of the Configuration page.</LI> <LI> <B>Level of tissue detail:</B> The <em>tissue</em> pulldown menu controls the amount and type of tissue data displayed. By default, the median of replicate tissues are shown. To display the value of all individual experimental replicates of all tissues, -select the <em>all replicates</em> option. +select the <em>all replicates</em> option.</LI> <LI> <B>Brightness:</B> To increase or decrease the brightness of the expression colors, edit the number in the column's <em>brightness</em> text box. Values greater than 1.0 increase the brightness, while those less than 1.0 dim the -color. +color. </LI> </UL></P> <H3>Methods</H3> <P> RNA (from a commercial source) from 11 tissues were hybridized to Affymetrix All Exon 1.0 ST arrays. For each tissue, 3 replicate experiments were done for a total of 33 arrays. The arrays' raw signal intensity was normalized with a quantile normalization method, then run through the PLIER algorithm. The normalized data were then converted to log-ratios, which are displayed as green for negative log-ratios (under-expression), and red for positive (over-expression).</P> <P>When calculating expression ratios, the overall expression level in the denominator was calculated by first taking the median of replicates for each tissue and then taking the median of these medians. </P> <P>