; >> (*) DETAILS: Turns out to be due to a single stray newline. It should
> have
> >> been
> >>
> >> affxparser::writeCdfUnits(...)
> >>
> >> but it was:
> >>
> >> affxparser::writeCdfUnits
> >> (...
its
>> (...)
>>
>> Despite running 24 hours of regular package testing, this piece of
>> code was never tested. I've now added an explicit test on creating
>> and re-creating monocell CDF.
>>
>> On Fri, Jan 23, 2015 at 8:49 AM, Henrik Ben
gt;
> affxparser::writeCdfUnits(...)
>
> but it was:
>
> affxparser::writeCdfUnits
> (...)
>
> Despite running 24 hours of regular package testing, this piece of
> code was never tested. I've now added an explicit test on creating
> and re-creating monoce
piece of
code was never tested. I've now added an explicit test on creating
and re-creating monocell CDF.
On Fri, Jan 23, 2015 at 8:49 AM, Henrik Bengtsson wrote:
> I managed to reproduce this now:
>
> Error in (...) : 3 arguments passed to '(' which requires 1
> 201501
I managed to reproduce this now:
Error in (...) : 3 arguments passed to '(' which requires 1
20150123 08:48:49| Could not locate monocell CDF. Will create one for chip type.
..done
20150123 08:48:49|Retrieving monocell CDF...done
> traceback()
5: .writeCdfUnits(con = con, srcU
gt; > So I have deleted the previous monocell cdf file in
annotationData/chipTypes/HG-U133_Plus_2 and re-create it by the following:
> >
> > cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2")
> >
> > cdfM <- getMonocellCdf(cdf, verbose = Arguments$getVerbos
= TRUE))
>
>
>
> However, the above process also failed, here is the output:
>
> > cdfM <- getMonocellCdf(cdf, verbose = Arguments$getVerbose(-8,
timestamp = TRUE))
>
> 20150123 21:47:53|Retrieving monocell CDF...
>
> 20150123 21:47:53| Monocell chip type: HG-U1
dfFile$byChipType("HG-U133_Plus_2")
cdfM <- getMonocellCdf(cdf, verbose = Arguments$getVerbose(-8, timestamp =
TRUE))
However, the above process also failed, here is the output:
> cdfM <- getMonocellCdf(cdf, verbose = Arguments$getVerbose(-8, timestamp
= TRUE))
20150123 21:
Hi Henrik,
Thank you very much for the information and it has clarified lot of my
doubts.
Best,
Sam.
On Thursday, January 22, 2015 at 8:36:59 PM UTC+1, Henrik Bengtsson wrote:
>
> Hi guys,
>
> here are some late feedback on this discussion:
>
> * When talking about copy numbers, it is importa
