I would like to do Rank Product analysis but get an error when I try this (see below):

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Error in AllButCelsForReadAffy(..., filenames = filenames, widget = widget, :
object 'PARAM_INPUTFILES' not found
Calls: ReadAffy -> AllButCelsForReadAffy
Execution halted

What can I do to resolve this?

Hi Rahul Patharkar,

to help me fix the problem it would be great if you could supply me with some more
information: Which version of Robin did you use? Did the quality checking step run
and finish without errors? Which affy chip type was your data generated on?

best greetings,
Marc

Hi Marc,

I just updated my JAVA and now Rank Product works! I am using the current version of Robin that can be downloaded, on Windows 7 64 bit with 32 bit JAVA. Before updating JAVA Robin could do quality checks and do linear analysis fine but gave an error when doing Rank Product. Thanks for responding quickly to my post and big thanks for making such a great program!

All the best,
Rahul

Hi Rahul,

i am happy to hear that it works now!

best greetings,
Marc

Hi Marc,

Actually Robin 1.3.0 (and 1.2.0) give an error when doing Rank Product analysis. Everything else seems to work fine. I made a mistake writing to you that updating JAVA fixes the problem. Actually I installed 1.1.7 in which Rank Product works. I have tried two computers (Windows 7, 32 bit JAVA) and found that both 1.3.0 and 1.2.0 do not do Rank Product correctly, however, 1.1.7 works on both computers. I am processing Arabidopsis Affy chips. One possible small bug I found in 1.1.7 is that the fold changes seem to be inverted (ie. negative log2ratios for increasing genes).

Thanks for your help on this,
Rahul

Hi Rahul,

i found the bug that was causing the rank product analysis to fail and fixed it. I will
bundle up new versions now and upload them to the web page tomorrow. Thanks
a lot for your feedback!

bests,
Marc

Marc,

Thank you very much for all your help! Robin is by far the easiest program I have used to process raw Affy chip data.

All the best,
Rahul