Dear Mark
thank you for your feedback and for reporting out this bug. Joseph
Barry (the cellHTS2 maintainer) pointed out that the method that
implements `channelNames<-` for NChannelSet objects (which is defined
in cellHTS2) is incompatible with the way NChannelSet manages itself;
this bad behaviour was probably introduced a long time ago (predating
Joe's involvement) and apparently not noticed because it is rarely
used.
For the time being, I recommend that you do not use the
`channelNames<-` method, and rather try to already create the object
with names that please you. Let us know if you need help with that.
We will remove the `channelNames<-` generic and method from the
cellHTS2 package. We will see whether it is possible/worthwhile to add
repaired versions of these to the Biobase package (which is where the
NChannelSet class is defined and where this generic function and
method definition really belong.)
Hope this helps, thanks for your feedback and patience again -
Wolfgang
On May 5, 2013, at 7:53 PM, Mark Dane <markdane08 at="" gmail.com=""> wrote:
> Hi Wolfgang,
>
> Thank you. I am learning this at several levels and I appreciate
your help.
>
> When I made the changes you provided, it renamed the channels within
the cellHTS object but then order them alphabetically. For instance,
>
>> channelNames(x) =
c('All#','G1/S','G2','M','Aneuploid','Apoptotic','cPARP','Envision')
>> channelNames(x)
> [1] "All#" "Aneuploid" "Apoptotic" "cPARP" "Envision"
"G1/S"
> [7] "G2" "M"
>
> This ordering shows up in the Plate List tab of the output of
writeReport. The file names and their data are in the correct order
but the channel names are not. This makes it appear that the channel
names are for the incorrect channel data.
>
> The boxplots in Plate Summaries are also reordered. Here they do
represent the correct data. This seems to be similar outcome to a
posting by Juliane Siebourg on 2012-06-05.
>
> Is gmane.org the best place to search for previously answered
cellHTS questions? I appreciate your direct mail answer. I'm just
unsure where the proper response (like this one) should go.
>
> thank you,
>
> Mark
>
> On May 5, 2013, at 9:02 AM, Wolfgang Huber <whuber at="" embl.de="">
wrote:
>
>> Dear Mark
>>
>> try
>>
>> channelNames(x) =
c('All#','G1/S','G2','M','Aneuploid','Apoptotic','cPARP','Envision')
>>
>> See also Section 2.1 of
http://cran.r-project.org/doc/manuals/r-release/R-intro.html
>>
>> Best wishes
>> Wolfgang
>>
>> On May 4, 2013, at 11:03 pm, Mark Dane <markdane08 at="" gmail.com="">
wrote:
>>
>>> Hi,
>>>
>>> I'm using cellHTS2 for a large siRNA screening project and want to
rename the channels. The cellHTS instance I created has the default
names:
>>>
>>>> channelNames(x)
>>> [1] "Channel 1" "Channel 2" "Channel 3" "Channel 4" "Channel 5"
"Channel 6"
>>> [7] "Channel 7" "Channel 8"
>>>
>>> The documentation in version 2.22.0 of Package 'cellHTS2' is:
>>>
>>> channelNames<-(object, value)
>>> signature(object = "cellHTS", value = "character"). Replace the
channel names in object.
>>>
>>> The way I interpret this, I think the following code should work:
>>>
>>> #create new names for the channels
>>> chnames=c('All#','G1/S','G2','M','Aneuploid','Apoptotic','cPARP','
Envision')
>>>
>>> #Assign the new names to the channels
>>> channelNames(x,chnames)
>>>
>>> The result is:
>>>
>>> Error in .local(object, ...) :
>>> unused argument (c("All#", "G1/S", "G2", "M", "Aneuploid",
"Apoptotic", "cPARP", "Envision"))
>>>
>>> Can you please explain the proper way to change the channel names?
>>>
>>>
>>> thank you for your help,
>>>
>>> Mark Dane
>>> Oregon Health and Sciences University
>>>
>>>
>>> Version info:
>>> version.string R version 3.0.0 (2013-04-03)
>>> cellHTS2_2.24.0
>>> [[alternative HTML version deleted]]
>>>
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>>
>
