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RGLab / flowWorkspace

flowWorkspace
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Namespace prefix on Workspace file/ Cant find samples when using Flowjo_to_gatingset #302

Open carl-coyle opened 4 years ago

carl-coyle commented 4 years ago

I can see that the error relating to namespace prefixes not being defined has been raised before. However I wasn't too sure from the answers what the solution was. I gathered that you can add back the namespace prefixes but I am just not aware how to actually do that in R. Forgive me I am very new to using R so i'm trying to learn as I go.

Currently I have some CyTOF data which I have cleaned up in FlowJo (Gated Singlets, live cells etc) I saved the workspace as an xml from the diagnostics toolbar in FlowJo and from what I can see on my R environment can load it in.

The error comes when I try open it using open_flowjo_xml. as you can see in the first image.

image

Although it seems to still create the workspace fine as it is listed in the envoirnment and when I search for samples and group names in it I get the information.

However when I try and parse the workspace with my FCS files it creates the following error in the other picture.

image

I'm wondering if one is related to the other??

Again apologies if this is all very obvious I am a very new user.

gfinak commented 4 years ago

sessionInfo() please. Specifically what versions of the flow packages (flowCore, flowWorkspace, CytoML, cytolib) are you using?

carl-coyle commented 4 years ago

[cid:47c5a552-8640-44fe-b4f8-959996c91cb6]

Please see image of session info.

[cid:e33d9b13-85f8-4d9a-991a-30dad7c92ff1]

The following is the versions of the above package's

Carl.

I should note I have now tried this with saving the Workspace as WSP and I no longer get the namespace error however it still seems i'm getting the no samples to be found error. Please see attached image.

[cid:7270425f-d7ac-43ed-9f79-6ab11064a423]

PhD Student. SpLab. Centre for Inflammation Biology & Cancer Immunology (CIBCI) King’s College London 1st floor New Hunt’s House, Guy’s Campus, London, SE1 1UL

From: Greg Finak notifications@github.com Sent: Tuesday, February 18, 2020 6:14 AM To: RGLab/flowWorkspace flowWorkspace@noreply.github.com Cc: Coyle, Carl carl.coyle@kcl.ac.uk; Author author@noreply.github.com Subject: Re: [RGLab/flowWorkspace] Namespace prefix on Workspace file/ Cant find samples when using Flowjo_to_gatingset (#302)

sessionInfo() please. Specifically what versions of the flow packages (flowCore, flowWorkspace, CytoML, cytolib) are you using?

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mikejiang commented 4 years ago

Can you check if those missing files do exist in the path that you specified?