Question: flowCore: retain raw data in the flowset after transformation
0
gravatar for carlos.x.martinez-fleites
8 months ago by

Hello,

Using flowcore functions, I would like to keep columns containing raw data in a flowset after applying a transformation, example:

logicleT <- logicleTransform( w = 0.5, t= 10000, m =4.5) transformation <- transformList(c("FL2-A", "FL3-A", "FL6-A", "FL10-A"), logicleT ) newFlowSet <- transform(flowset, transformation)

If done as above, newFlowSet will contain flowframes with columns with transformed data and not the original data.

Is it possible at all to retain the original columns and add new columns with the transformed values?

Many thanks.

flowcore flow cytometry • 190 views
ADD COMMENTlink modified 8 months ago by Jiang, Mike1.2k • written 8 months ago by carlos.x.martinez-fleites0
Answer: flowCore: retain raw data in the flowset after transformation
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gravatar for Jiang, Mike
8 months ago by
Jiang, Mike1.2k
(Private Address)
Jiang, Mike1.2k wrote:

You can do inline transformation,e.g.

newFlowSet <- transform(flowset, `trans-FL2-A` = logicleT(`FL2-A`), `trans-FL3-A` = logicleT(`FL3-A`))

By the way, why do you need the original columns?

ADD COMMENTlink written 8 months ago by Jiang, Mike1.2k

Thanks, this works nicely.

I want to keep all columns in the flowset for subsequent conversion into a single data.frame that I use as a data source for ggplot.

ADD REPLYlink written 8 months ago by carlos.x.martinez-fleites0
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