(Back to the public forum)
REPRODUCIBLE EXAMPLE:
It's a bug (still to be found) that shows itself when one runs the
analysis in one directory up from the root /, e.g. /arom-anal/. I
managed to reproduce this by running a standard analysis in /tmp/.
WORKAROUND:
Run the analysis in directory that
I've narrowed down this bug to the R.utils package and fixed it. I've
verified that the RMA pipeline now also works running in /tmp/.
Update aroma.affymetrix (including R.utils) by running:
source(http://callr.org/install#aroma.affymetrix;)
in a fresh R session.
/Henrik
On Tue, Sep 16, 2014
That is really odd and I've never seen that error (8-9 years now).
There must be a simple answer to this. What does:
print(plm)
print(getwd())
output when you get to that step.
/Henrik
On Tue, Sep 16, 2014 at 9:38 PM, jjspring OH sshshoh1...@gmail.com wrote:
Hi,
After setting up the
Ok, and then the output of:
path - getPath(plm)
print(path)
dir(plmData)
isDirectory(plmData)
Arguments$getReadablePath(plmData)
/H
On Tue, Sep 16, 2014 at 9:57 PM, jjspring OH sshshoh1...@gmail.com wrote:
Hi Henrik,
See below:
print(plm)
RmaPlm:
Data set: tissues
Chip type:
Hi Henrik,
See the outputs:
path - getPath(plm)
print(path)
[1] plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1
dir(plmData)
[1] tissues,RBC,QN,RMAtissues,RBC,QN,RMA,merged
isDirectory(plmData)
[1] TRUE
Arguments$getReadablePath(plmData)
[1] plmData
2014년 9월 17일 수요일
