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SPADE: Spanning Tree Progression of Density Normalized Events
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Execution halted!!! #43

Closed cfozza closed 12 years ago

cfozza commented 12 years ago

Hello!

Im trying to run on SPADE some FCS data generated with FACSDiva Software from BD.

CytoSPADE generates the R script successfully but when running the SPADE analysis I get the following error message:

Warning message: No function found corresponding to methods exports from 'rrcov' for: 'show' Downsampling file: ./Bal_Tube_001.fcs Warning message: In readBin(con = con, what = dattype, n = count, size = size, signed = signed, : 'signed = FALSE' is only valid for integers of sizes 1 and 2 Execution halted

Could ypu please help me?

Many thanks and congratulations on your great work!

Claudio

AlixDahirel commented 12 years ago

Hi Claudio,

I'm not a spade expert but I just got the same bug and solved it following the guidlines indicated here: nolanlab/spade#39

esimonds commented 12 years ago

Yes, Alix's suggestion should work -- Claudio please let us know if that solves your problem. Alix, thanks for helping the community!

cfozza commented 12 years ago

Many thanks for your suggestions!

Unfortunately, after reinstalling all tha packages step by step I have experienced a new error message:

Errore in checkSlotAssignment(object, name, value) : assignment of an object of class "numeric" is not valid for slot "transformationId" in an object of class "transform"; is(value, "character") is not TRUE Calls: -> @<- -> slot<- -> checkSlotAssignment Execution halted

Please note I'm working on a Windows XP 32-bit.

Any further advise? Really sorry to disturb you again...

zbjornson commented 12 years ago

Hello Claudio -- I'm guessing you're on a computer that uses commas as the decimal indicator? Please see here: https://github.com/nolanlab/spade/issues/42#issuecomment-8817934 The comment above that one has an example of the runSPADE.R file if you want to compare.

Thanks, Zach

zbjornson commented 12 years ago

Hello again -- I've updated the FAQ here with a full list of recommendations: https://github.com/nolanlab/spade/wiki/FAQ See FAQ # 7 there.

Best, Zach

cfozza commented 12 years ago

Hi Zach!

I am afraid I am the worst Spade user... Could please suggest me how to open my runSPADE.R file?

rbruggner commented 12 years ago

It is actually just a text file so you can just open it using any program that edits text.

If you are on Mac, I would suggest TextEdit.app. If PC, then probably Notepad?

-Rob

On Sep 25, 2012, at 8:33 AM, cfozza notifications@github.com wrote:

Hi Zach!

I am afraid I am the worst Spade user... Could please suggest me how to open my runSPADE.R file?

— Reply to this email directly or view it on GitHub.

zbjornson commented 12 years ago

Hi Claudio,

Nonsense -- my apologies for not giving clearer advice.

  1. Once you've gone through the Cytoscape wizard and you've arrived at the last page called "Summary and Run," there are two buttons: "Generate runSPADE Script" and "Run SPADE." Click only "Generate runSPADE Script."
  2. Open the folder that has your FCS files in Windows Explorer (as you would get to your documents, for example). There should now be a new file called "runSPADE.R". Right-click and select "Open with notepad." Now go through and change the commas to periods in the TRANSFORMS line.

Hopefully we'll have the plugin fixed shortly so you won't have to do this.

Best, Zach

cfozza commented 12 years ago

Thanks again for being so patient...unfortunately, after doing everything you suggested me, I get this message:

BEGIN AUTOGENERATED DATA

FILE_TO_PROCESS="." CLUSTERING_MARKERS=c("APC-Cy7-A","PE-Cy7-A","PerCP-Cy5-5-A") PANELS=list(

  • list(
  • panel_files=c("Bal_Tube_001.fcs"),
  • median_cols=NULL,
  • reference_files=NULL,
  • fold_cols=NULL
  • )) TRANSFORMS=flowCore::arcsinhTransform(a=0, b=0,006667) Scalable Robust Estimators with High Breakdown Point (version 1.3-02)

Errore in checkSlotAssignment(object, name, value) : assignment of an object of class "numeric" is not valid for slot "transformationId" in an object of class "transform"; is(value, "character") is not TRUE Calls: -> @<- -> slot<- -> checkSlotAssignment Esecuzione interrotta

And if, after running SPADE, I check the file in which I have changed the commas into periods (I have also saved this change), they are changed back to commas!

zbjornson commented 12 years ago

In my steps listed earlier, after you click "Generate runSPADE Script," do not close that window. Minimize/work around Cytoscape while you do step #2. Then, back in Cytoscape, click the "runSPADE" button. The key is to not re-run the wizard after you've changed the commas to periods.

Thanks! Zach

cfozza commented 12 years ago

Actually, I am not re-running it...I am afraid I have done it correctly, without closing the window...

zbjornson commented 12 years ago

Hrm. You're positive you're modifying the correct runSPADE.R file in the correct directory? Sorry -- have to ask :)

cfozza commented 12 years ago

I am very happy you double check me...it is a runSPADE file in which I have changed to: TRANSFORMS=flowCore::arcsinhTransform(a=0. b=0.006667)

zbjornson commented 12 years ago

I'm not sure what the problem is at this point. I'll try to fix the plugin today so that you don't have to do any modifications to the file. Stand by please...

cfozza commented 12 years ago

Thanks so much for all your help!!!

Dr. Claudio Fozza, MD Aggregate Professor, Blood Diseases Haematology Unit Department of Biomedical Sciences University of Sassari Viale San Pietro 12 07100 Sassari Italy Tel. +39 079 228592 Fax. +39 079 228282 Email address: cfozza@uniss.it

---------- Original Message ----------- From: Zach Bjornson notifications@github.com To: nolanlab/spade spade@noreply.github.com Cc: cfozza cfozza@uniss.it Sent: Tue, 25 Sep 2012 10:31:25 -0700 Subject: Re: [spade] Execution halted!!! (#43)

I'm not sure what the problem is at this point. I'll try to fix the plugin today so that you don't have to do any modifications to the file. Stand by please... — Reply to this email directly or view it on GitHub. ------- End of Original Message -------

zbjornson commented 12 years ago

Hi Claudio,

Please try this:

  1. Download this file: https://github.com/nolanlab/spade/raw/master/inst/tools/CytoSPADE.jar
  2. Put that file in your Cytoscape plugins directory. This is probably C:\Program Files\Cytoscape_v2.8.3\plugins for you. Click "ok" or "replace" to acknowledge that you're replacing the existing file with the same name.
  3. Restart Cytoscape and run the wizard again. In the final screen when it shows a large white text box with your selected parameters, the flowcore::arcsinhTransform(...) line should have a decimal instead of a comma now.

Thanks! Zach

cfozza commented 12 years ago

Hi Zach!

Still no working...

Now I correctly see "Transformation:  flowCore::arcsinh(a=0.0, b=0.007)" in the Summary and Run window. But when I run spade the execution is halted and if I check back the runSPADE.R file, it has been changed again to "TRANSFORMS=flowCore::arcsinhTransform(a=0, b=0,006667)".

---------- Original Message ----------- From: Zach Bjornson notifications@github.com To: nolanlab/spade spade@noreply.github.com Cc: cfozza cfozza@uniss.it Sent: Tue, 25 Sep 2012 11:43:02 -0700 Subject: Re: [spade] Execution halted!!! (#43)

Hi Claudio, Please try this:

  • Download this file: https://github.com/nolanlab/spade/raw/master/inst/tools/CytoSPADE.jar
  • Put that file in your Cytoscape plugins directory. This is probably C:\Program Files\Cytoscape_v2.8.3\plugins for you. Click "ok" or "replace" to acknowledge that you're replacing the existing file with the same name.
  • Restart Cytoscape and run the wizard again. In the final screen when it shows a large white text box with your selected parameters, the flowcore::arcsinhTransform(...) line should have a decimal instead of a comma now.

Thanks! Zach — Reply to this email directly or view it on GitHub. ------- End of Original Message -------

zbjornson commented 12 years ago

Hi Claudo, sorry -- didn't really have a way to test it here. I think I just fixed the output as well. Please try those same steps again. Thanks, Zach

zbjornson commented 12 years ago

Hello again Claudio, Another user with the same issue with commas and periods has confirmed that this issue is fixed in the latest version of the plugin. You can either follow the steps I posted earlier, or reinstall SPADE using the instructions in the wiki.

Thanks, Zach

cfozza commented 12 years ago

Hi Zach! I have just reinstalled R, Cytoscape and SPADE step by step...and now it works...

Thanks so much!!!