Entering edit mode
Yesterday it was brought to my attention that SigCheck 2.2.0 had regressed substantially from the previous release (SigCheck 2.0.1), with a nearly empty vignette. This situation has now been rectified, so please use SigCheck 2.2.1 or later (or 2.3.1 on the development branch). I apologize for any inconvenience.
Also note that the Mac and Windows binaries have not yet been automatically rebuilt, so you will have to wait a bit before that happens, unless you can install them from source. I will update this thread as the new binaries become available.
Cheers-
Rory
P.S. I have also added a section to the vignette explaining how to get known gene signatures from MSigDB (Broad GSEA). You have to accept their licence and download the signatures.
2.2.1 binaries for Mac OSX 10.9 (Mavericks) and later are now available.
Windows binary is available for 2.2.1.
Hi Rory Stark
I am grateful for your nice package sigcheck, I am using this package to test my signature, but I have a problem, it is very time consuming,I think it is better to tell you more about my signature, it has 98 genes and I test its performance in some independent studies, and also I checked it performance with sigcheck. I ran these codes
> check <- sigCheck(nki, classes="e.os", survival="t.os",signature=mysig,
+ annotation="HUGO.gene.symbol",validationSamples=which(nki$series=="NKI2"))
and it gave me to km plot quickly(train and validation), but in the next step I ran
and after 24 h it still working, I read in sigcheck reference manual that the sigChekcall function needs more time but I doubt about my case ,is it normal or there is a problem?
Thanks in advance