From a6b27a094474535732f5da3a951c8377b584cfc2 Mon Sep 17 00:00:00 2001 From: hvaret Date: Mon, 28 Aug 2017 15:30:45 +0200 Subject: [PATCH] bulletPoints --- DESCRIPTION | 4 ++-- NEWS | 4 ++++ inst/report_DESeq2.rmd | 6 +++--- inst/report_edgeR.rmd | 6 +++--- 4 files changed, 12 insertions(+), 8 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 8a7d82b..0833684 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: SARTools Type: Package Title: Statistical Analysis of RNA-Seq Tools -Version: 1.5.0 -Date: 2017-08-10 +Version: 1.5.1 +Date: 2017-08-28 Author: Marie-Agnes Dillies and Hugo Varet Maintainer: Hugo Varet Depends: R (>= 3.3.0), DESeq2 (>= 1.12.0), edgeR (>= 3.12.0), xtable diff --git a/NEWS b/NEWS index 2676cd8..21368c1 100755 --- a/NEWS +++ b/NEWS @@ -1,3 +1,7 @@ +CHANGES IN VERSION 1.5.1 +------------------------ + o fixed a bug in bullet points + CHANGES IN VERSION 1.5.0 ------------------------ o new HTML report (dynamic table of contents, automatic bibliography) diff --git a/inst/report_DESeq2.rmd b/inst/report_DESeq2.rmd index 72ca217..7aa0fa5 100755 --- a/inst/report_DESeq2.rmd +++ b/inst/report_DESeq2.rmd @@ -242,9 +242,9 @@ These files contain the following columns: - `r paste(paste(levels(target[,varInt])[-nlevels(target[,varInt])],collapse=", "),levels(target[,varInt])[nlevels(target[,varInt])],sep=" and ")`: means (rounded) of normalized counts of the biological conditions; - FoldChange: fold change of expression, calculated as $2^{\log_2(\text{FC})}$; - log2FoldChange: $\log_2(\text{FC})$ as estimated by the GLM model. It reflects the differential expression between Test and Ref and can be interpreted as $\log_2(\frac{\text{Test}}{\text{Ref}})$. If this value is: - + around 0: the feature expression is similar in both conditions; - + positive: the feature is up-regulated ($\text{Test} > \text{Ref}$); - + negative: the feature is down-regulated ($\text{Test} < \text{Ref}$); + + around 0: the feature expression is similar in both conditions; + + positive: the feature is up-regulated ($\text{Test} > \text{Ref}$); + + negative: the feature is down-regulated ($\text{Test} < \text{Ref}$); - pvalue: raw p-value from the statistical test; - padj: adjusted p-value on which the cut-off $\alpha$ is applied; - dispGeneEst: dispersion parameter estimated from feature counts (i.e. black dots on figure 11); diff --git a/inst/report_edgeR.rmd b/inst/report_edgeR.rmd index 3a4c95b..6bc45d2 100755 --- a/inst/report_edgeR.rmd +++ b/inst/report_edgeR.rmd @@ -226,9 +226,9 @@ These files contain the following columns: - `r paste(paste(levels(target[,varInt])[-nlevels(target[,varInt])],collapse=", "),levels(target[,varInt])[nlevels(target[,varInt])],sep=" and ")`: means (rounded) of normalized counts of the biological conditions; - FoldChange: fold change of expression, calculated as $2^{\log_2(\text{FC})}$; - log2FoldChange: $\log_2(\text{FC})$ as estimated by the GLM model. It reflects the differential expression between Test and Ref and can be interpreted as $\log_2(\frac{\text{Test}}{\text{Ref}})$. If this value is: - + around 0: the feature expression is similar in both conditions; - + positive: the feature is up-regulated ($\text{Test} > \text{Ref}$); - + negative: the feature is down-regulated ($\text{Test} < \text{Ref}$); + + around 0: the feature expression is similar in both conditions; + + positive: the feature is up-regulated ($\text{Test} > \text{Ref}$); + + negative: the feature is down-regulated ($\text{Test} < \text{Ref}$); - pvalue: raw p-value from the statistical test; - padj: adjusted p-value on which the cut-off $\alpha$ is applied; - tagwise.dispersion: dispersion parameter estimated from feature counts (i.e. black dots on figure 9);