Question: Summarization process on HT HG-U133 Plus PM array
0
gravatar for itzirurzun
5.0 years ago by
itzirurzun0
Spain
itzirurzun0 wrote:

Hi!

I'm trying to analyse some microarray data from HT HG-U133 Plus PM chip, but I've problems in the summarization process. I've already done the background correction and the normalization with tools from aroma.affymetrix package, but an error ocurred in the summarization part when it has to create the monocell CDF file.

I'm using RMAPlm function like this for the summarization:

plm <- RmaPlm(csN)
fit(plm, verbose=verbose)

It tells me: error in (...) : 3 arguments passed to '(' which requires 1

I don't know how to fix this, so if someone could help me I'll be very thankful.

 

ADD COMMENTlink modified 5.0 years ago by Henrik Bengtsson60 • written 5.0 years ago by itzirurzun0
2
gravatar for Henrik Bengtsson
5.0 years ago by
United States
Henrik Bengtsson60 wrote:

This is a known bug in aroma.affymetrix 2.13.0.  Updating to 2.13.1 should fix this. Update with:

source('http://callr.org/install#aroma.affymetrix')
ADD COMMENTlink written 5.0 years ago by Henrik Bengtsson60

Thanks! 

But now I have problems updating the package... The error that appeared is the next one:

Error in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  : 
  type == "both" cannot be used if 'available' or 'contriburl' is specified

When I install other package I never had this type of problems, I don't know if it is because I have to update the package as an admin or what..

Are you familiar with this problem?

Thanks in advanced!

ADD REPLYlink written 5.0 years ago by itzirurzun0

At the end I manage to install the last version of the package and now the summarization process is working!!

Thanks a lot!!!

ADD REPLYlink written 4.9 years ago by itzirurzun0

I'm having the same problem - can you tell me how you managed to fix it?  Thanks!

Edit: Nevermind, solved it.  For anyone else having the same problem, I installed the required packages using install.packages(), which worked.

 

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by Lisa.Hopcroft0
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