CoCAS, with Agilent micro arrays

[blackos]

Hi,

I'm using CoCAS for my chip-on-chip analysis and I have an insolvent problem.

Here is a link to download CoCAS :

http://www.ciml.univ-mrs.fr/software/cocas/index.html

During analysis, it seems that CoCAS can not read the column "rMeanSignal" of my raw data, but this column is present on my file (i checked it with "cut -f 34 file.txt...") :

----------------------------------------------------
Start Analysis...

Reading Files...

Read E:/result.TXT
Arrays of slide 1 have been read. (no Dye-swap)

Intra-Arrays Normalization Start...

Slide 1

computing p valuesErreur dans var(Xlow[which(Xlow < 0)]) : 'x' est vide
De plus : Warning message:
In read.maimages(noSwap, source = "generic", columns = list(R = "rMeanSignal", :
non-standard columns specified

-----------------------------------------


Is somebody have already the same problem ? Thank you a lot for your help !!!

[blackos]

Hi,

I'm trying to install the linux version. I installed the R libraries, and when I launch the following command :

java -jar COCAS_v2.4.jar

I've got this error :

Exception in thread "main" java.lang.NoClassDefFoundError: org/rosuda/JRI/RMainLoopCallbacks
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:634)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:277)
at java.net.URLClassLoader.access$000(URLClassLoader.java:73)
at java.net.URLClassLoader$1.run(URLClassLoader.java:212)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
Caused by: java.lang.ClassNotFoundException: org.rosuda.JRI.RMainLoopCallbacks
at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
... 11 more


Can somebody help me to install this software ? Thank you again for your help !!!

[blackos]

Hello !

I just solved my first problem :

the "SystematicName" column must respect the syntax :"chrX:9numbers:9numbers".

Have fun.