SigCheck 2.2.0 regression: please use 2.2.1 and later!
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Rory Stark ★ 5.2k
@rory-stark-5741
Last seen 1 day ago
Cambridge, UK

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.

SigCheck sigcheck • 1.4k views
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2.2.1 binaries for Mac OSX 10.9 (Mavericks) and later are now available.

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Windows binary is available for 2.2.1.

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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

Results <- sigCheckAll(check, iterations=1000)

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

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