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nolanlab / citrus

Citrus Development Code
GNU General Public License v3.0
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No output in sam_results #80

Closed bc2zb closed 7 years ago

bc2zb commented 8 years ago

When sourcing the runCitrus.R file generate by the GUI. Nothing prints to the sam_results directory, and only markerPlots.pdf and markerPlotsAll.pdf are being outputted by the script. Is this the expected behavior?

shenorr commented 8 years ago

Yes if no diiferencrs noted by fdr of 10% On Aug 27, 2015 6:17 PM, "bc2zb" notifications@github.com wrote:

When sourcing the runCitrus.R file generate by the GUI. Nothing prints to the sam_results directory, and only markerPlots.pdf and markerPlotsAll.pdf are being outputted by the script. Is this the expected behavior?

— Reply to this email directly or view it on GitHub https://github.com/nolanlab/citrus/issues/80.

bc2zb commented 8 years ago

Thanks for the quick response. One other question, what is the significance of the following error? I have not encountered it before, and can't seem to find anyone else who has either.

Error in ttstar[, j] <- -1 * sort(-1 * ttstar[, j]) : replacement has length zero

shenorr commented 8 years ago

By the look of the code this is an error internal to SAM - what did you try to do? On Aug 27, 2015 6:28 PM, "bc2zb" notifications@github.com wrote:

Thanks for the quick response. One other question, what is the significance of the following error? I have not encountered it before, and can't seem to find anyone else who has either.

Error in ttstar[, j] <- -1 * sort(-1 * ttstar[, j]) : replacement has length zero

— Reply to this email directly or view it on GitHub https://github.com/nolanlab/citrus/issues/80#issuecomment-135469254.

bc2zb commented 8 years ago

I ran the code at the bottom of the runCitrus.R file. The section with the heading below:

==================================================================================================

The following lines perform the same analysis as the citrus.full() function but broken down

into component steps. This is may be more useful to run if you plan on running the clustering

once but examining many endpoints, features, or minimum cluster sizes. You should uncomment

the clustering, feature extraction, regression, and plotting functionlines.

==================================================================================================

I uncommented the places where appropriate. The error comes up whenever I run the following command from the script:

citrus.regressionResults = mclapply(modelTypes,citrus.endpointRegress,citrus.foldFeatureSet=citrus.foldFeatureSet,labels=labels,family=family)

I will have many cytof runs coming across my desk, so I am trying to build a pipeline with Citrus. The GUI is very nice but would not work well for my pipeline.