Hi Nishant,

I have made the corrections to plateCore suggested by the reviewer.
I appreciate the reviewer taking the time to thoroughly examine the plateCore package.
My responses to the reviewer's comments are provided below.

Errol

> I have several comments that may help the authors improve the package:
> The antibody identities in the example data are masked, which introduces
> confusion for a knowledgeable analyst.  I recommend that only patient
> identifiers be masked and that the original antibody assignments be used in the
> vignette and the example data.  This will make it much more interpretable for a
> skilled cytometrist.  The plate data on the FICCS website (at least the version
> that I downloaded almost a year ago) would be suitable for this purpose.

The layout of the antibody-dye conjugates on the 96-well plate is proprietary to BD.   
We agree that providing the antibody assignments would the the data much more interesting, 
but we do not yet have approval to release the layout. 

> I found some errors in the help pages.  For example, the compensate document
> page refers to flowCore:compensate, but the link is broken.  Same on the
> compensationSet page.

I've updated the help pages so they are compatible with the latest version of flowCore.

> PlotPlate is not illustrated in the vignette.  The help page says ?this type of
> plot is not very useful but people like to make them?.
> gutterPlot seemed to have some formatting problems running on Linux with an
> x11() display.

I was not able to replicate the formatting problems since gutterPlot renders
correctly in Windows XP and in Ubuntu 32-bit. In the example, the data is pretty
well behaved and they are no wells that would be flagged based on gutterPlot.
Perhaps the reviewer is referring to the compactness of the points on
the y-axis? 

> In the vignette I studied Figure 2 fairly carefully.  I cannot see any visual
> differences at all between the original and background-corrected plots.  It?s
> not a good illustration of the utility of this function.  Recommend omitting it
> or finding a better (worse?) example with more autofluorescence.
> In this same section of the vignette some editing is needed:  ?This correction
> will later allows us to de?ne a one-dimensional gate between positive and
> negative cells in only the channel (of) interest, instead of having a two
> dimensional gate that includes the forward scatter (FSC) channel. The background
> correction uses the unstained wells and ?ts a log-log linear model to FSC versus
> each ?uorescence channel (Insert Florian?s ref ).?

I was unable to find a publicly available data set where the autofluorescence correction
had a big effect. This correction isn't required for PBMCs, but it make analysis
of adherent cells (fibroblasts, stem cells, etc.) much easier. Unfortunately, 
we are not able to release data on these other cell types. Even though we can't
make a compelling case to correct for autofluorescence with PBMC data, we think it is 
important provide an example. I increased the autofluorescence in the PBMC lymphocyte
example in Figure 2 so that readers can see how the method functions.

> I executed on a Leopard platform the code on page 9 that supposedly generates
> Figure 1 (the Figure would be better placed with the code that generates it).  I
> got an error: ?Error using packet x, method for function ?glpoints?, for
> signature ?intersectFilter?? in the graphical window, where x = the panel number
> 1:4.

It appears that plotting intersect filters (rectGate & normGate) is not working correctly for xyplot on
flowSets from the flowViz package. I changed the functions to use xyplot for 
flowPlates instead, and edited the text to reflect the changes. I'll investigate
why the function call fails on flowSets.

> For Figure 3 it would be helpful to illustrate the use of the getGroups() method
> to select the wells associated with the negative control for A03.  As it is, the
> figure shown is not the result of the code shown above it ? in my opinion, bad
> form for a vignette.  In general Sweave is such a cool thing ? why not use it?
> Section 7 would be better if each of the figures produced by the xyplot were
> included in the vignette.

I edited the vignette so that the code use to generate the figure is in the text.
Also, I used this figure to illustrate the use of the getGroups() function. 

> The documentation for flowPlate, flowPlate-class, and flowPlate-flowSet-method
> are all the same.  Generally, the man page for flowPlate should describe the
> constructor, and flowPlate-class should describe the object slots and methods
> for S4 classes.  The constructor can be documented in the class page, but please
> don?t omit a complete description of the class.  For example, the subset
> operators [ and [[  should be documented in the class document.  See
> flowCore::flowFrame-class documentation for a good example.

I separated the documentation for the flowPlate constructor documentation from the flowPlate class.
The flowPlate class documentation was modeled on the flowSet-class example, providing
the slots and subset operators. 

> Authorship is not clear.  The DESCRIPTION file indicates Strain and Haaland.
> The vignette suggests just Strain.  The plateCore-package man page indicates
> Strain, Hahne and Haaland.

Authorship of the vignette and Description file have been updated to include
all 3 authors.