This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Summarization process on HT HG-U133 Plus PM array

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 occurred 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.

ht-hg-u133-plus-pm summarization affymetrix
• 3,266 views • link
updated by Ram Ram • written by itzirurzun • itzirurzun

1 answer

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')
• 0 views • link
updated by Ram Ram • written by Henrik Bengtsson • Henrik Bengtsson

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 advance!

• 0 views • link
updated by Ram Ram • written by itzirurzun • itzirurzun

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

Thanks a lot!!!

• 0 views • link
written by itzirurzun • itzirurzun

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

Edit: Never mind, solved it. For anyone else having the same problem, I installed the required packages using install.packages(), which worked.

• 0 views • link
updated by Ram Ram • written by Lisa.Hopcroft • Lisa.Hopcroft

Log in to answer this question.

More posts like this