Help with GenePix files
1
0
Entering edit mode
@heike-pospisil-1097
Last seen 10.2 years ago
Hello, it's the first time I am dealing with two-color microarrays. That is why I have some (probably stupid) questions... I am trying to analyze GenePix files using the marrayInput package and I ran into two difficulties: 1) I have 24 GenePix-arrays that are defined by three different *.gal-files. Can I merge the expressions for these three types of arrays for the upcoming normalization step? 2) Does someone know the error message "Error in if (skip > 0) readLines(file, skip) : missing value where TRUE/FALSE needed" and has a hint for avoiding it? > galinfo<-read.Galfile("3kArray5.gal") > myTargets <- read.marrayInfo(file.path(data.dir, "target.txt")) target.txt: Name Cy3 Cy5 a.gpr 10D 14D ar.gpr 14D 10D > read.GenePix(c("a.gpr","ar.gpr"),targets=myTargets,layout=galinfo$layo ut,gnames=galinfo$gnames,) Reading ... a.gpr Error in if (skip > 0) readLines(file, skip) : missing value where TRUE/FALSE needed Unfortunately, I have no idea what could be the reason for this error message. I would be very glad about any suggestion. Thanks in advance and best wishes, Heike PS: I am using R2.3.1 and marray version 1.12.0. -- Dr. Heike Pospisil | pospisil at zbh.uni-hamburg.de University of Hamburg | Center for Bioinformatics Bundesstrasse 43 | 20146 Hamburg, Germany phone:+49-40-42838-7303 | fax: +49-40-42838-7312
Normalization marray GLAD Normalization marray GLAD • 1.2k views
ADD COMMENT
0
Entering edit mode
Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 10.2 years ago
Hi Heike, > PS: I am using R2.3.1 and marray version 1.12.0. The first thing you need to do is to upgrade your R and install the latest marray package. Then give another try. If you still have problems, send another note. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org
ADD COMMENT

Login before adding your answer.

Traffic: 576 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6