diff --git a/DESCRIPTION b/DESCRIPTION
index 6878f3b..c69a29e 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: SARTools
 Type: Package
 Title: Statistical Analysis of RNA-Seq Tools
-Version: 1.6.6
-Date: 2018-10-04
+Version: 1.6.7
+Date: 2019-05-07
 Author: Marie-Agnes Dillies and Hugo Varet
 Maintainer: Hugo Varet <hugo.varet@pasteur.fr>
 Depends: R (>= 3.3.0), DESeq2 (>= 1.12.0), edgeR (>= 3.12.0), xtable
diff --git a/NEWS b/NEWS
index 88d6ff5..45ea8a3 100755
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,8 @@
+CHANGES IN VERSION 1.6.7
+------------------------
+        o modified the installation guidelines for the Bioconductor packages
+	o new parameters in the MAPlot() and volcanoPlot() functions thanks to Ken Field suggestion on GitHub
+
 CHANGES IN VERSION 1.6.6
 ------------------------
 	o fixed a bug introduced in version 1.6.4 when giving featureCounts files as input
diff --git a/R/MAPlot.R b/R/MAPlot.R
index b8bfc38..db4827f 100755
--- a/R/MAPlot.R
+++ b/R/MAPlot.R
@@ -5,10 +5,11 @@
 #' @param complete A \code{list} of \code{data.frame} containing features results (from \code{exportResults.DESeq2()} or \code{exportResults.edgeR()})
 #' @param alpha cut-off to apply on each adjusted p-value
 #' @param outfile TRUE to export the figure in a png file
+#' @param log2FClim numeric vector containing both upper and lower y-axis limits for all the MA-plots produced (NULL by default to set them automatically)
 #' @return A file named MAPlot.png in the figures directory containing one MA-plot per comparison
 #' @author Marie-Agnes Dillies and Hugo Varet
 
-MAPlot <- function(complete, alpha=0.05, outfile=TRUE){
+MAPlot <- function(complete, alpha=0.05, outfile=TRUE, log2FClim=NULL){
   ncol <- ifelse(length(complete)<=4, ceiling(sqrt(length(complete))), 3)
   nrow <- ceiling(length(complete)/ncol)
   if (outfile) png(filename="figures/MAPlot.png", width=cairoSizeWrapper(1800*ncol), height=cairoSizeWrapper(1800*nrow), res=300)
@@ -18,7 +19,11 @@ MAPlot <- function(complete, alpha=0.05, outfile=TRUE){
         complete.name <- complete.name[complete.name$baseMean>0,]
         complete.name$padj <- ifelse(is.na(complete.name$padj),1,complete.name$padj)
         log2FC <- complete.name$log2FoldChange
-        ylim <- 1.1 * c(-1,1) * quantile(abs(log2FC[is.finite(log2FC)]), probs=0.99)
+        if (is.null(log2FClim)){
+          ylim <- 1.1 * c(-1,1) * quantile(abs(log2FC[is.finite(log2FC)]), probs=0.99)
+        } else{
+          ylim <- log2FClim
+        }
         plot(complete.name$baseMean, pmax(ylim[1], pmin(ylim[2], log2FC)),
 	         log = "x", cex=0.45, las = 1, ylim = ylim,
              col = ifelse(complete.name[,"padj"] < alpha, "red", "black"),
diff --git a/R/cairoSizeWrapper.R b/R/cairoSizeWrapper.R
old mode 100644
new mode 100755
diff --git a/R/summarizeResults.DESeq2.r b/R/summarizeResults.DESeq2.r
index 393792a..897cfac 100755
--- a/R/summarizeResults.DESeq2.r
+++ b/R/summarizeResults.DESeq2.r
@@ -8,11 +8,14 @@
 #' @param cooksCutoff outliers detection threshold (TRUE to let DESeq2 choosing it or FALSE to disable the outliers detection)
 #' @param alpha significance threshold to apply to the adjusted p-values
 #' @param col colors for the plots
+#' @param log2FClim numeric vector containing both upper and lower y-axis limits for all the MA-plots produced (NULL by default to set them automatically)
+#' @param padjlim numeric value between 0 and 1 for the adjusted p-value upper limits for all the volcano plots produced (NULL by default to set them automatically)
 #' @return A list containing: (i) a list of \code{data.frames} from \code{exportResults.DESeq2()}, (ii) the table summarizing the independent filtering procedure and (iii) a table summarizing the number of differentially expressed features
 #' @author Hugo Varet
 
 summarizeResults.DESeq2 <- function(out.DESeq2, group, independentFiltering=TRUE, cooksCutoff=TRUE,
-                                    alpha=0.05, col=c("lightblue","orange","MediumVioletRed","SpringGreen")){
+                                    alpha=0.05, col=c("lightblue","orange","MediumVioletRed","SpringGreen"),
+                                    log2FClim=NULL, padjlim=NULL){
   # create the figures/tables directory if does not exist
   if (!I("figures" %in% dir())) dir.create("figures", showWarnings=FALSE)
   if (!I("tables" %in% dir())) dir.create("tables", showWarnings=FALSE)
@@ -50,10 +53,10 @@ summarizeResults.DESeq2 <- function(out.DESeq2, group, independentFiltering=TRUE
   rawpHist(complete=complete)
   
   # MA-plots
-  MAPlot(complete=complete, alpha=alpha)
+  MAPlot(complete=complete, alpha=alpha, log2FClim=log2FClim)
  
   # Volcano plots
-  volcanoPlot(complete=complete, alpha=alpha)
+  volcanoPlot(complete=complete, alpha=alpha, padjlim=padjlim)
  
   return(list(complete=complete, tabIndepFiltering=tabIndepFiltering, nDiffTotal=nDiffTotal))
 }
diff --git a/R/summarizeResults.edgeR.r b/R/summarizeResults.edgeR.r
index cc0d738..0017954 100755
--- a/R/summarizeResults.edgeR.r
+++ b/R/summarizeResults.edgeR.r
@@ -7,11 +7,14 @@
 #' @param counts matrix of raw counts
 #' @param alpha significance threshold to apply to the adjusted p-values
 #' @param col colors for the plots
+#' @param log2FClim numeric vector containing both upper and lower y-axis limits for all the MA-plots produced (NULL by default to set them automatically)
+#' @param padjlim numeric value between 0 and 1 for the adjusted p-value upper limits for all the volcano plots produced (NULL by default to set them automatically)
 #' @return A list containing: (i) a list of \code{data.frames} from \code{exportResults.edgeR()} and (ii) a table summarizing the number of differentially expressed features
 #' @author Hugo Varet
 
 summarizeResults.edgeR <- function(out.edgeR, group, counts, alpha=0.05,
-                                   col=c("lightblue","orange","MediumVioletRed","SpringGreen")){  
+                                   col=c("lightblue","orange","MediumVioletRed","SpringGreen"),
+                                   log2FClim=NULL, padjlim=NULL){  
   # create the figures/tables directory if does not exist
   if (!I("figures" %in% dir())) dir.create("figures", showWarnings=FALSE)
   if (!I("tables" %in% dir())) dir.create("tables", showWarnings=FALSE)
@@ -34,10 +37,10 @@ summarizeResults.edgeR <- function(out.edgeR, group, counts, alpha=0.05,
   rawpHist(complete=complete)
   
   # MA-plots
-  MAPlot(complete=complete, alpha=alpha)
+  MAPlot(complete=complete, alpha=alpha, log2FClim=log2FClim)
   
   # Volcano plots
-  volcanoPlot(complete=complete, alpha=alpha)
+  volcanoPlot(complete=complete, alpha=alpha, padjlim=padjlim)
   
   return(list(complete=complete, nDiffTotal=nDiffTotal))
 }
diff --git a/R/volcanoPlot.r b/R/volcanoPlot.r
index 8f81e65..f75bf00 100755
--- a/R/volcanoPlot.r
+++ b/R/volcanoPlot.r
@@ -5,10 +5,11 @@
 #' @param complete A \code{list} of \code{data.frame} containing features results (from \code{exportResults.DESeq2()} or \code{exportResults.edgeR()})
 #' @param alpha cut-off to apply on each adjusted p-value
 #' @param outfile TRUE to export the figure in a png file
+#' @param padjlim numeric value between 0 and 1 for the adjusted p-value upper limits for all the volcano plots produced (NULL by default to set them automatically)
 #' @return A file named volcanoPlot.png in the figures directory containing one volcano plot per comparison
 #' @author Hugo Varet
 
-volcanoPlot <- function(complete, alpha=0.05, outfile=TRUE){
+volcanoPlot <- function(complete, alpha=0.05, outfile=TRUE, padjlim=NULL){
   ncol <- ifelse(length(complete)<=4, ceiling(sqrt(length(complete))), 3)
   nrow <- ceiling(length(complete)/ncol)
   if (outfile) png(filename="figures/volcanoPlot.png", width=cairoSizeWrapper(1800*ncol), height=cairoSizeWrapper(1800*nrow), res=300)
@@ -17,7 +18,11 @@ volcanoPlot <- function(complete, alpha=0.05, outfile=TRUE){
       complete.name <- complete[[name]]
       complete.name$padj[which(complete.name$padj==0)] <- .Machine$double.xmin
       log10pval <- -log10(complete.name$padj)
-      ylim <- c(0,1) * quantile(log10pval, probs=0.99, na.rm=TRUE)
+      if (is.null(padjlim)){
+        ylim <- c(0,1) * quantile(log10pval, probs=0.99, na.rm=TRUE)
+      } else{
+        ylim <- c(0,1) * -log10(padjlim)
+      }
       plot(complete.name$log2FoldChange, pmin(ylim[2], log10pval), ylim=ylim, las=1, cex=0.45,
            xlab=expression(log[2]~fold~change), ylab=expression(-log[10]~adjusted~P~value),
            col=ifelse(complete.name$padj <= alpha, "red", "black"), pch=ifelse(log10pval >= ylim[2], 2, 20),
diff --git a/README.md b/README.md
index 9263734..6032330 100755
--- a/README.md
+++ b/README.md
@@ -13,7 +13,7 @@ How to install SARTools?
 In addition to the SARTools package itself, the workflow requires the installation of several packages: DESeq2, edgeR, genefilter, xtable and knitr (all available online, see the dedicated webpages). SARTools needs R version 3.3.0 or higher, DESeq2 1.12.0 or higher and edgeR 3.12.0 or higher: old versions of DESeq2 or edgeR may be incompatible with SARTools.
 
 To install the SARTools package from GitHub, open a R session and:
-- install DESeq2, edgeR and genefilter with `source("http://bioconductor.org/biocLite.R")` and `biocLite(c("DESeq2", "edgeR", "genefilter"))` (if not installed yet)
+- install DESeq2, edgeR and genefilter with `if (!requireNamespace("BiocManager")){install.packages("BiocManager")}` and `BiocManager::install(c("DESeq2", "edgeR", "genefilter"))` (if not installed yet)
 - install devtools with `install.packages("devtools")` (if not installed yet)
 - Notes:
 
diff --git a/man/MAPlot.Rd b/man/MAPlot.Rd
index cd4145d..d85bc9e 100644
--- a/man/MAPlot.Rd
+++ b/man/MAPlot.Rd
@@ -4,7 +4,7 @@
 \alias{MAPlot}
 \title{MA-plots}
 \usage{
-MAPlot(complete, alpha = 0.05, outfile = TRUE)
+MAPlot(complete, alpha = 0.05, outfile = TRUE, log2FClim = NULL)
 }
 \arguments{
 \item{complete}{A \code{list} of \code{data.frame} containing features results (from \code{exportResults.DESeq2()} or \code{exportResults.edgeR()})}
@@ -12,6 +12,8 @@ MAPlot(complete, alpha = 0.05, outfile = TRUE)
 \item{alpha}{cut-off to apply on each adjusted p-value}
 
 \item{outfile}{TRUE to export the figure in a png file}
+
+\item{log2FClim}{numeric vector containing both upper and lower y-axis limits for all the MA-plots produced (NULL by default to set them automatically)}
 }
 \value{
 A file named MAPlot.png in the figures directory containing one MA-plot per comparison
diff --git a/man/summarizeResults.DESeq2.Rd b/man/summarizeResults.DESeq2.Rd
index 63d7f95..b990d9b 100644
--- a/man/summarizeResults.DESeq2.Rd
+++ b/man/summarizeResults.DESeq2.Rd
@@ -6,7 +6,7 @@
 \usage{
 summarizeResults.DESeq2(out.DESeq2, group, independentFiltering = TRUE,
   cooksCutoff = TRUE, alpha = 0.05, col = c("lightblue", "orange",
-  "MediumVioletRed", "SpringGreen"))
+  "MediumVioletRed", "SpringGreen"), log2FClim = NULL, padjlim = NULL)
 }
 \arguments{
 \item{out.DESeq2}{the result of \code{run.DESeq2()}}
@@ -20,6 +20,10 @@ summarizeResults.DESeq2(out.DESeq2, group, independentFiltering = TRUE,
 \item{alpha}{significance threshold to apply to the adjusted p-values}
 
 \item{col}{colors for the plots}
+
+\item{log2FClim}{numeric vector containing both upper and lower y-axis limits for all the MA-plots produced (NULL by default to set them automatically)}
+
+\item{padjlim}{numeric value between 0 and 1 for the adjusted p-value upper limits for all the volcano plots produced (NULL by default to set them automatically)}
 }
 \value{
 A list containing: (i) a list of \code{data.frames} from \code{exportResults.DESeq2()}, (ii) the table summarizing the independent filtering procedure and (iii) a table summarizing the number of differentially expressed features
diff --git a/man/summarizeResults.edgeR.Rd b/man/summarizeResults.edgeR.Rd
index 627f3ab..da61372 100644
--- a/man/summarizeResults.edgeR.Rd
+++ b/man/summarizeResults.edgeR.Rd
@@ -5,7 +5,8 @@
 \title{Summarize edgeR analysis}
 \usage{
 summarizeResults.edgeR(out.edgeR, group, counts, alpha = 0.05,
-  col = c("lightblue", "orange", "MediumVioletRed", "SpringGreen"))
+  col = c("lightblue", "orange", "MediumVioletRed", "SpringGreen"),
+  log2FClim = NULL, padjlim = NULL)
 }
 \arguments{
 \item{out.edgeR}{the result of \code{run.edgeR()}}
@@ -17,6 +18,10 @@ summarizeResults.edgeR(out.edgeR, group, counts, alpha = 0.05,
 \item{alpha}{significance threshold to apply to the adjusted p-values}
 
 \item{col}{colors for the plots}
+
+\item{log2FClim}{numeric vector containing both upper and lower y-axis limits for all the MA-plots produced (NULL by default to set them automatically)}
+
+\item{padjlim}{numeric value between 0 and 1 for the adjusted p-value upper limits for all the volcano plots produced (NULL by default to set them automatically)}
 }
 \value{
 A list containing: (i) a list of \code{data.frames} from \code{exportResults.edgeR()} and (ii) a table summarizing the number of differentially expressed features
diff --git a/man/volcanoPlot.Rd b/man/volcanoPlot.Rd
index 2243243..57398d9 100644
--- a/man/volcanoPlot.Rd
+++ b/man/volcanoPlot.Rd
@@ -4,7 +4,7 @@
 \alias{volcanoPlot}
 \title{Volcano plots}
 \usage{
-volcanoPlot(complete, alpha = 0.05, outfile = TRUE)
+volcanoPlot(complete, alpha = 0.05, outfile = TRUE, padjlim = NULL)
 }
 \arguments{
 \item{complete}{A \code{list} of \code{data.frame} containing features results (from \code{exportResults.DESeq2()} or \code{exportResults.edgeR()})}
@@ -12,6 +12,8 @@ volcanoPlot(complete, alpha = 0.05, outfile = TRUE)
 \item{alpha}{cut-off to apply on each adjusted p-value}
 
 \item{outfile}{TRUE to export the figure in a png file}
+
+\item{padjlim}{numeric value between 0 and 1 for the adjusted p-value upper limits for all the volcano plots produced (NULL by default to set them automatically)}
 }
 \value{
 A file named volcanoPlot.png in the figures directory containing one volcano plot per comparison
diff --git a/template_script_DESeq2.r b/template_script_DESeq2.r
index c592f67..5c893ab 100755
--- a/template_script_DESeq2.r
+++ b/template_script_DESeq2.r
@@ -2,7 +2,7 @@
 ### R script to compare several conditions with the SARTools and DESeq2 packages
 ### Hugo Varet
 ### March 20th, 2018
-### designed to be executed with SARTools 1.6.6
+### designed to be executed with SARTools 1.6.7
 ################################################################################
 
 ################################################################################
diff --git a/template_script_DESeq2_CL.r b/template_script_DESeq2_CL.r
index 390a5e0..e509f8b 100755
--- a/template_script_DESeq2_CL.r
+++ b/template_script_DESeq2_CL.r
@@ -2,7 +2,7 @@
 ### R script to compare several conditions with the SARTools and DESeq2 packages
 ### Hugo Varet
 ### March 20th, 2018
-### designed to be executed with SARTools 1.6.6
+### designed to be executed with SARTools 1.6.7
 ### run "Rscript template_script_DESeq2_CL.r --help" to get some help
 ################################################################################
 
diff --git a/template_script_edgeR.r b/template_script_edgeR.r
index 0e71063..82ec7da 100755
--- a/template_script_edgeR.r
+++ b/template_script_edgeR.r
@@ -2,7 +2,7 @@
 ### R script to compare several conditions with the SARTools and edgeR packages
 ### Hugo Varet
 ### March 20th, 2018
-### designed to be executed with SARTools 1.6.6
+### designed to be executed with SARTools 1.6.7
 ################################################################################
 
 ################################################################################
diff --git a/template_script_edgeR_CL.r b/template_script_edgeR_CL.r
index 3527159..b0f3945 100755
--- a/template_script_edgeR_CL.r
+++ b/template_script_edgeR_CL.r
@@ -2,7 +2,7 @@
 ### R script to compare several conditions with the SARTools and edgeR packages
 ### Hugo Varet
 ### May 16th, 2018
-### designed to be executed with SARTools 1.6.6
+### designed to be executed with SARTools 1.6.7
 ### run "Rscript template_script_edgeR_CL.r --help" to get some help
 ################################################################################