Question: Subsetting and Transforming
gravatar for smajor
2.8 years ago by
smajor0 wrote:


I'm working through the flowCore manual  "flowCore: data structures package for flow cytometry data, N. Le Meur F. Hahne B. Ellis P. Haaland, December 1, 2016" 

In section 4.3 Subsetting it instructs to give the code 

> morphGate <- norm2Filter("FSC-H", "SSC-H", filterId="MorphologyGate",
> smaller <- Subset(fs, morphGate)  # fs is a flowSet
> fs[[1]]

When I input my flowSet, it doesn 't work unless I specify a specific flowFrame,

The error I get:

> morphGate <- norm2Filter("FSC-A","SSC-A", filterId = "MorphologyGate",
                         scale= 2)
> smaller <- Subset(set,morphGate) # set is a non-transformed flowSet
# Error in y[, 1] : incorrect number of dimensions

Up until this point, the flow set has been running fine with the previous code with the same flowSet.

Thank you!

flowcore subsetting gate • 451 views
ADD COMMENTlink modified 2.8 years ago by Martin Morgan ♦♦ 24k • written 2.8 years ago by smajor0
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