Question

Passing truncate_max_range=FALSE to read.ncdfFlowSet

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alavy ▴ 30

@alavy-23451

Last seen 4.6 years ago

Hi, I am new to flow cytometry and to flowcore / ncdfFlow so I apologize if I missed anything when reading the documentation.

When I load single flow frames with read.FCS I can pass the argument to keep max ranges, so this command works well:

fr <- read.FCSfile.name, alter.names=TRUE, transformation=FALSE, truncate_max_range=FALSE)

I understand from the man page that read.ncdfFlowSet should accept read.FCS arguments but it seems to ignore truncate_max_range=FALSE

ncfs  <- read.ncdfFlowSet(fcsFiles, alter.names=TRUE, transformation=FALSE, truncate_max_range=FALSE)

The output I get is identical to when I read a single frame with truncate_max_range=TRUE

Is there another way to include the maximum range?

Thanks! Adi

ncdfFlow flowCore ncdfFlowSet read.FCS • 1.9k views

ADD COMMENT • link updated 4.6 years ago by Jake Wagner ▴ 310 • written 4.6 years ago by alavy ▴ 30

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update: When loading the data with the truncate_max_range=FALSE argument and looking at one of the frames, the max range is shown to be 4, whereas when executing a summary command, it shows a maximum value of 5

ncfs  <- read.ncdfFlowSet(fcsFiles, alter.names=TRUE, transformation=FALSE, truncate_max_range=FALSE)
fr <- ncfs[[6]]
fr
flowFrame object '2019-02-07_at_03-07-59pm.F04.fcs'


summary(fr)

        Parameter_15 Parameter_16 Parameter_17
Min.        0.000000     0.000000       1719.0
1st Qu.     2.139012     4.999991     899891.2
Median      2.397036     4.999991    1839945.0
Mean        2.301236     4.581938    1851571.8
3rd Qu.     2.608794     4.999991    2829041.2
Max.        4.486561     4.999991    3790363.0
with 5000 cells and 17 observables:
             name       desc   range    minRange maxRange
$P1   Parameter_1   FSC-HLin   26336  100.218422    26335
$P2   Parameter_2   SSC-HLin   55118   11.853891    55117
$P3   Parameter_3 GRN-B-HLin   99998    0.000000    99997
$P4   Parameter_4 YEL-B-HLin   99998    0.000000    99997
$P5   Parameter_5 RED-B-HLin   47876    0.000000    47875
$P6   Parameter_6 RED-R-HLin   23877    0.000000    23876
$P7   Parameter_7 RED-R-ALin   30659    0.015429    30658
$P8   Parameter_8    RED-R-W   99998    0.000000    99997
$P9   Parameter_9   FSC-HLog       4    2.000947        3
$P10 Parameter_10   SSC-HLog       4    1.073861        3
$P11 Parameter_11 GRN-B-HLog       4    0.000000        3
$P12 Parameter_12 YEL-B-HLog       4    0.000000        3
$P13 Parameter_13 RED-B-HLog       4    0.000000        3
$P14 Parameter_14 RED-R-HLog       4    0.000000        3
$P15 Parameter_15 RED-R-ALog       4    0.000000        3
$P16 Parameter_16 RED-R-WLog       4    0.000000        3
$P17 Parameter_17       TIME 3790363 1719.000000  3790362
121 keywords are stored in the 'description' slot

ADD REPLY • link 4.6 years ago alavy ▴ 30

score 2 · Accepted Answer · 2020-04-29

The different ranges are probably just coming from the fact that the minRange and maxRange are coming from the instrument defined range min and max (in the $PnR value of the FCS) as opposed to the min/max taken from the actual data. You can specify which to use within the range method by passing type="data" or type="instrument" (default). For example:

fr <- read.FCS(fcs_file_path)
range(fr) # will default to instrument range
range(fr, type = "data") # Will use the actual values, as in summary

If you're still seeing disagreement with the ncdfFlowSet you are reading in after specifying which min/max to report, please let me know and provide your session info and the code snippet that reproduces it. In my testing, truncate_max_range is working as expected for both read.FCS and read.ncdfFlowSet.