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Issue creating a GatingSet #341
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How do you propose we try to reproduce your error? |
First, try the code below to see if it succeeds library(flowCore)
library(flowWorkspace)
data("GvHD")
fs <- GvHD[1:2]
gs <- GatingSet(fs)
gs Then, provide some more context of your use case and code, paste the |
@mikejiang the code you posted works for me, no problem. However, I also am getting the same error as @santoshe1 and this is a (relatively) new problem. I will provide you with a test case that works and a test case that does not work, complete with sample data, tomorrow. |
@mikejiang in Experiment 1, a flowset is created successfully but we fail to create a gatingset, with the same error as reported above by @santoshe1.
In Experiment 2, both flowset and gatingset are created successfully.
Complete test cases: https://drive.google.com/drive/folders/1JJWsCYgMjPeWVFKBm0GfXMp2gTlLDb3I |
It should be noted that while I was expecting Furthermore, it appears that creating an
... to have the metadata fields populated. Otherwise they are filled with I understand that this is not an issue with flowWorkspace per se, but if we then take this This can all be reproduced with the test case files provided above. |
It was due to the head(rownames(pData))
[1] "Experiment1_data/786 n1/786n1_Ca1uM4h_samp_20x 00016119 613.LMD"
[2] "Experiment1_data/786 n1/786n1_Ca1uM4h_samp_60x 00016122 616.LMD"
[3] "Experiment1_data/786 n1/786n1_Ca1uM4h_samp_100x 00016125 619.LMD" This causes the trouble for flowset <- read.flowSet(
+ dataset=1,
+ transformation=FALSE,
+ alter.names=TRUE,
+ phenoData = phenoData
+ )
>
> sampleNames(flowset)
[1] "Experiment1_data_786 n1_786n1_Ca1uM4h_samp_20x 00016119 613.LMD"
[2] "Experiment1_data_786 n1_786n1_Ca1uM4h_samp_60x 00016122 616.LMD"
[3] "Experiment1_data_786 n1_786n1_Ca1uM4h_samp_100x 00016125 619.LMD" so now it should work for gatingset <- GatingSet(flowset)
> head(sampleNames(gatingset))
[1] "Experiment1_data_786 n1_786n1_Ca1uM4h_samp_20x 00016119 613.LMD"
[2] "Experiment1_data_786 n1_786n1_Ca1uM4h_samp_60x 00016122 616.LMD"
[3] "Experiment1_data_786 n1_786n1_Ca1uM4h_samp_100x 00016125 619.LMD" Try to pull the latest |
@mikejiang Ohhhhhhhhh my godddd hahaha. Brilliant, thank you so much! I had been wrestling with this for many hours yesterday and just could not figure it out. I appreciate the quick fix! |
I'm getting the same error, but I'm not sure if I've installed the packages correctly. I ran these:
And then again I got:
|
Scratch that, I restarted my environment and everything seems to work correctly! |
Command -
> fs_transformed A flowSet with 130 experiments.
gs <- GatingSet(fs_transformed)
I get an error:
Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'GatingSet': unimplemented type 'list' in 'EncodeElement'
Kindly assist. Thanks
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