Re: [aroma.affymetrix] [process and display function in aroma.affymetrix]

2014-09-20 Thread Henrik Bengtsson
On Sat, Sep 20, 2014 at 9:11 PM, jjspring OH wrote: > > > Thanks! Yes, it seems it is due to old version for manual example, > > > Everything is done when i follow the URL for now and getting display(ae) > result (attached file) > BTW just checking out for one warning message from plm fitting befo

Re: [aroma.affymetrix] [process and display function in aroma.affymetrix]

2014-09-20 Thread Henrik Bengtsson
How are you setting up the ArrayExplorer? It looks like you're missing to set the color maps. Are you following a particular example (URL?) that could be wrong. Have a look at http://www.aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis for an example. /Henrik On Sat, Sep 20, 2014 at

Re: [aroma.affymetrix] [process and display function in aroma.affymetrix]

2014-09-20 Thread jjspring OH
And also, For process(ae) getting warning messages(pls see below) it seems to be related with next command lines it does not matter? could you please take a closer look at these as well? curent sessionInfo is R version 3.1.1 (2014-07-10) Platform: x86_64-apple-darwin10.8.0 (64-bit) local

Re: [aroma.affymetrix] [process and display function in aroma.affymetrix]

2014-09-19 Thread Henrik Bengtsson
On Fri, Sep 19, 2014 at 8:24 AM, Henrik Bengtsson wrote: > Sorry, it took me a while to spot the actual problem; > >> display(ae) >> The file >> /foo/arom-anal/\foo\arom-anal\reports\tissues\RBC,QN,RMA\ArrayExplorer.html >> does not exist. > > (I'm surprised there is no "error" or similar genera

Re: [aroma.affymetrix] [process and display function in aroma.affymetrix]

2014-09-19 Thread Henrik Bengtsson
Sorry, it took me a while to spot the actual problem; > display(ae) > The file > /foo/arom-anal/\foo\arom-anal\reports\tissues\RBC,QN,RMA\ArrayExplorer.html > does not exist. (I'm surprised there is no "error" or similar generated, but it could be because that message is from an external softwa

[aroma.affymetrix] [process and display function in aroma.affymetrix]

2014-09-17 Thread jjspring OH
Hi, I am getting errors when i run aroma.affymetrix package for dynamic reports, it looks like for low level analysis, everything works well for now, Could you please take a closer look at and let me know what the problem is? I am running under the current directory(/foo/arom-anal/) > proce