From 192f76e53f1c76d0ccee210af3815883d09f4c5f Mon Sep 17 00:00:00 2001 From: robwwilliams Date: Fri, 19 Feb 2021 08:19:44 -0600 Subject: Update Wang_WIlliams_Rat_Brain_Proteome_For_Blog.md --- blog/2021/proteome/Wang_WIlliams_Rat_Brain_Proteome_For_Blog.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/blog/2021/proteome/Wang_WIlliams_Rat_Brain_Proteome_For_Blog.md b/blog/2021/proteome/Wang_WIlliams_Rat_Brain_Proteome_For_Blog.md index 8286db9..912c99d 100644 --- a/blog/2021/proteome/Wang_WIlliams_Rat_Brain_Proteome_For_Blog.md +++ b/blog/2021/proteome/Wang_WIlliams_Rat_Brain_Proteome_For_Blog.md @@ -15,7 +15,7 @@ Wang (University of North Dakota) and colleagues, including Jumin Peng at St. Jude Children\'s Research Hospital, and Michal Pravenec at the Czech Academy of Science. This is an open, but not yet final, quantitative proteomics data for the whole brain for 21 strains of rat -(male and female isogenic littermates) from the HXB/BXH family---part of +(male and female isogenic littermates) from the HXB/BXH family--part of the Hybrid Rat Diversity Panel. For those of you on this list at NIH, first, thank you for all of your @@ -224,11 +224,11 @@ like this:  Beneath the Manahattan plot there is a **Mapping Statistics** table that provides estimates a SNP coordinates (Rnor6 assembly) calculated by -GEMMA with --logP values and additive effects (log2 scale). +GEMMA with -logP values and additive effects (log2 scale). ![](media/image10.png) -A --logP value of 5.27 is good---normally at or above genome-wide +A -logP value of 5.27 is good---normally at or above genome-wide threshold of significance. (This assertion does need more support, and we are testing thresholds using using other mapping methods, including R/qtl\'s and WebQTL\'s standard interval mapping methods, and using @@ -239,7 +239,7 @@ protein expression quantitative trait locus (QTL) on Chr 1? To answer this question we need to sort the **Mapping Statistics** by the **Position** column. Once sorted, we have to decide how wide a confidence interval is appropriate given the density of DNA variants, -gene density, and --logP values. Karl Broman and others recommend a drop +gene density, and -logP values. Karl Broman and others recommend a drop in the --logP linkage statistic of about 1.5 on either side of the peak, or plateau in this case. For the QTL map of SYT7 the confidence interval encompasses an stretch of DNA from about 35 megabases (Mb) to 43 Mb. -- cgit v1.2.3