Matching markers in COMPASSContainerFromGatingSet()

[Scott1009]

I have some issues turning a GatingSetList into a COMPASS Container
Previous to this, I merged several GatingSets given the examples at:
http://www.bioconductor.org/packages/3.7/bioc/vignettes/flowWorkspace/inst/doc/HowToMergeGatingSet.html
There seems to be a mismatch between markers requested, and markers returned.

In these two cases when I ask for DUMP, I get data for IL-4, and when I ask for IL-4, it is not found.
(it's not a one off problem, all markers seem to be mis-matched)
Does this represent a problem with the code, or potentially a problem with the data?

Any comments would be helpful.

> foo <- COMPASSContainerFromGatingSet(L, 'Memory/CD154+ CD69+', individual_id = "sampleId", markers=c("DUMP"))
Extracting cell counts
Fetching CD154+ CD69+
Fetching child nodes
common markers are: 
CXCR3 DUMP IL-4 CD4 CCR7 CD45RA IL-17 CD69 CCR6 CD3 TNF CD154 IFNg CCR4 CD8 IL-2 
We will map the following nodes to markers:
Extracting single cell data for Memory/CD154+ CD69+/IL-4+
...................................................................................................................................................................................................................................Creating COMPASS Container
Filtering low counts
Filtering 75 samples due to low counts
> foo <- COMPASSContainerFromGatingSet(L, 'Memory/CD154+ CD69+', individual_id = "sampleId", markers=c("IL-4"))
Extracting cell counts
Fetching CD154+ CD69+
Fetching child nodes
common markers are: 
CXCR3 DUMP IL-4 CD4 CCR7 CD45RA IL-17 CD69 CCR6 CD3 TNF CD154 IFNg CCR4 CD8 IL-2 
We will map the following nodes to markers:
Extracting single cell data for NA
Error in .cpp_getNodeID(obj@pointer, sampleNames(obj)[1], y) : 
  NA not found!

[gfinak]

Hard to say.. I'll have to step through the code, it's been a while since I've touched this particular piece. Can you reproduce this with small gating set constructed from a subset of samples (say 2 or 3), and use clone() to get an independent hdf5 file? If so, that could give me something small to work with and try to identify the issue. Best Greg Greg Finak

…

On Dec 21, 2017 10:41, "Scott Presnell" ***@***.***> wrote: I have some issues turning a GatingSetList into a COMPASS Container Previous to this, I merged several GatingSets given the examples at: http://www.bioconductor.org/packages/3.7/bioc/vignettes/ flowWorkspace/inst/doc/HowToMergeGatingSet.html There seems to be a mismatch between markers requested, and markers returned. In these two cases when I ask for DUMP, I get data for IL-4, and when I ask for IL-4, it is not found. (it's not a one off problem, all markers seem to be mis-matched) Does this represent a problem with the code, or potentially a problem with the data? Any comments would be helpful. > foo <- COMPASSContainerFromGatingSet(L, 'Memory/CD154+ CD69+', individual_id = "sampleId", markers=c("DUMP")) Extracting cell counts Fetching CD154+ CD69+ Fetching child nodes common markers are: CXCR3 DUMP IL-4 CD4 CCR7 CD45RA IL-17 CD69 CCR6 CD3 TNF CD154 IFNg CCR4 CD8 IL-2 We will map the following nodes to markers: Extracting single cell data for Memory/CD154+ CD69+/IL-4+ ...................................................................................................................................................................................................................................Creating COMPASS Container Filtering low counts Filtering 75 samples due to low counts > foo <- COMPASSContainerFromGatingSet(L, 'Memory/CD154+ CD69+', individual_id = "sampleId", markers=c("IL-4")) Extracting cell counts Fetching CD154+ CD69+ Fetching child nodes common markers are: CXCR3 DUMP IL-4 CD4 CCR7 CD45RA IL-17 CD69 CCR6 CD3 TNF CD154 IFNg CCR4 CD8 IL-2 We will map the following nodes to markers: Extracting single cell data for NA Error in .***@***.***, sampleNames(obj)[1], y) : NA not found! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#59>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABUkebUjIOP9-T6xNYb1hSQ8blCkVtLnks5tCqZtgaJpZM4RKM9b> .