I've updated aroma.affymetrix v2.11.8 and friends. Update by:
source(http://callr.org/install#aroma.affymetrix;)
I'd be keen to hear whether this solves your problem or not.
/Henrik
On Thu, Sep 4, 2014 at 1:47 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote:
Hi,
good that it works for you
Hi Henrik:
Thank you for patching this so quickly. I didn't realize the defaults of
file.copy() had changed in R 2.13.0.
I'll test this once my current job (n = ~400 CEL files) is complete, and
I'll let you know what I find.
Taylor
On Friday, September 5, 2014 4:15:56 PM UTC-4, Henrik
Hi Henrik:
Thank you for the prompt reply. You are right- the .CEL files are all read
only (see their permissions, below)
rtraborn@Mason:
/N/dc2/scratch/rtraborn/ML_Project/NIK_2014/rawData/NIK_2014/HuEx-1_0-st-v2
ls -lkhtra
-r--r--r-- 1 ... 63M Jan 25 2011 GSM709338_HSB194-VFC-R.CEL
Hi,
good that it works for you with this workaround. The fix in aroma is
fairly simple(*). I'll let you know when an updated version is
available.
(*) DETAILS: This has to do with base::file.copy() and its argument
'copy.mode' which was introduced in R 2.13.0 (April 2011). The thing
is that
