@@ -1,5 +1,5 @@

 Package: DEsubs

-Version: 1.1.0

+Version: 1.1.1

 Date: 2015-07-19

 Title: DEsubs: an R package for flexible identification of

         differentially expressed subpathways using RNA-seq expression

@@ -1 +1,3 @@

-...

\ No newline at end of file

+1.1.1: - Update in User Guide/User Input

+

+1.1.0: - Initial version

\ No newline at end of file

@@ -58,7 +58,7 @@ if (.Platform[['OS.type']] == 'windows')

 }

 ```

-Now the packake, as well as the toy-data can be loaded as follows:

+Now the package, as well as the toy-data can be loaded as follows:

 ```{r eval=FALSE, echo=TRUE}

 library('DEsubs')

@@ -88,7 +88,7 @@ load(system.file('extdata', 'data.RData', package='DEsubs'))

 \newpage

 ## 2. User Input

-DEsubs accepts RNA-seq expression control-case profile data. The following 

+DEsubs accepts RNA-seq expression paired case-control profile data. The following 

 example in Table 1 shows the right structure for RNA-seq expression data input.

@@ -103,7 +103,7 @@ data <- c(    1879, 2734, 2369, 2636, 2188, 9743, 9932, 10099,

 data <- matrix(data, nrow=6, ncol=8, byrow=TRUE)

 rownames(data) <- c(paste0('Gene ', 1:3), '...',  'Gene N-1', 'Gene N')

-colnames(data) <- paste0('Sample ', 1:8)

+colnames(data) <- c(paste0('Case ', 1:4), paste0('Control ', 1:4))

 kable( data,

     caption = 'Example of user input format' )