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nolanlab / citrus

Citrus Development Code
GNU General Public License v3.0
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"No thresholds for SAM" error #27

Closed esimonds closed 10 years ago

esimonds commented 10 years ago

Maybe I'm configuring the analysis incorrectly, but I got the error below. I got the same exact error when I tried again with a simpler analysis (5 files in each group, sampling 500 cells per file).

My runCitrus.R and citrusOutput.log are on gist here: https://gist.github.com/esimonds/d1ecaf424da8cd7dc930

Error text snipped from log file:

Calculating threshold deviance rates Calculating CV minima Extracting differential features Error in sigGenes[, "Fold Change"] : incorrect number of dimensions In addition: Warning message: In FUN("sam"[[1L]], ...) : No thresholds for SAM.

rbruggner commented 10 years ago

The "No thresholds for SAM" is not actually an error, but this may be a problem with dealing with SAM results that only return a single significant feature. Tried to fix in c45c8e1f0d5e8e9f31548cdcccb1caced2276fe6.

Run install_github("citrus","nolanlab") and see if it still breaks with the new changes?

esimonds commented 10 years ago

OK with the new version, it now says:

Calculating threshold deviance rates Calculating CV minima Extracting differential features Plotting Error Rate Plotting Stratifying Features Plotting Stratifying Clusters Plotting Clustering Graph Warning message: In FUN("sam"[[1L]], ...) : No thresholds for SAM. This is Normal.

If you want to test it yourself, the dataset and citrusOutput folder are on Blanca in /tmp/FCS_Files

rbruggner commented 10 years ago

That is the expected behavior. If you don’t see any output in the citrusOutput directory, then I don’t think it found any results :\

On Dec 7, 2013, at 3:26 PM, Erin Simonds notifications@github.com wrote:

OK with the new version, it now says:

Calculating threshold deviance rates Calculating CV minima Extracting differential features Plotting Error Rate Plotting Stratifying Features Plotting Stratifying Clusters Plotting Clustering Graph Warning message: In FUN("sam"[[1L]], ...) : No thresholds for SAM. This is Normal.

If you want to test it yourself, the dataset and citrusOutput folder are on Blanca in /tmp/FCS_Files

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esimonds commented 10 years ago

There's output in sam_results -- I just wasn't sure what to make of it given the error message. Thanks for clarifying it!