Hi All,
I think I have to add these too to my previous message about qcReport
error.
After getting the error, I tried to go on and try next steps.
I was able to get the control Indexes but again got an error message
at
controlQC step:
cqc<- controlQC(rawData=rawData, controlIndex= ctrlIdx,
IDcol="sampleID",
expcol="tissue", ylimits=c(-6,8), outfile= "boxplots_check.pdf",
height=7,
width=9)
Spatial normalization
Background removal
Error in density.default(x, kernel = "epanechnikov", n=n.pts,
na.rm=TRUE):
need at least 2 points to select a bandwidth automatically
I got this error previously, but unfortunately could not get an answer
from
the list. I think it is about the memory. If it is about memory (which
on
our machine is 47.2 GiB), how can I solve this problem? Maybe parallel
computing may do?
Any help will be much appreciated.
Best,
Zeynep
On Sat, Apr 5, 2014 at 1:38 PM, zeynep özkeserli
<zeynep.ozkeserli@gmail.com> wrote:
> Hi all (and if any chance, Dr. Aryee),
>
> I am working with 112 (56 532, 56 635) NimbleGen Promoter Medip
arrays to
> perform a CHARM analysis.
>
> First of all, I wanted to obtain the qc values and have a qcReport
but I
> get this error message:
>
> Error in plot.window(...) : need finite 'xlim' values
>
> My code is:
>
> dataDir<- getwd()
> pd<- readDelim( files=pd$fileName, path=dataDir, sampleKey=pd)
> rawData<- readCharm(files=pd$fileName, path=dataDir, sampleKey=pd)
> qual<- qcReport(rawData, file="qcReport.pdf")
>
> R version: 3.03
> Memory: 47.2 GiB
> Processor: Intel Xeon CPU E5645 @ 2.40GHz x 19
> OS type: 64-bit
> Disk. 146.2 GB
>
> Has anyone have any idea about this?
>
> Thank you in advance,
>
> Best,
>
> Zeynep
>
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