SPADE is not working

[horowitzamir]

Dear Erin and Michael,

I have been using SPADE for a while now. Not sure if you remember, but you had sent me a link for the developer's version that would allow me to self-correct the color scales more easily because my boss is color blind. I actually really find it less desirable than the original. I have tried to re-downlaod the cytospade plugin, but now the entire program is not working. I have tried on my own for some time now. I was wondering if either of you have a spare moment this week, if I could stop by your lab with my Macbook to get this downloaded with the original version, i.e. blue = negative and red=positive.

Thanks very much

Amir

[esimonds]

Hi Amir,

I'll be in the lab tomorrow. I'll reply to you privately with directions.

Erin

On Wed, Jan 18, 2012 at 5:50 PM, horowitzamir < reply@reply.github.com

wrote:

Dear Erin and Michael,

I have been using SPADE for a while now. Not sure if you remember, but you had sent me a link for the developer's version that would allow me to self-correct the color scales more easily because my boss is color blind. I actually really find it less desirable than the original. I have tried to re-downlaod the cytospade plugin, but now the entire program is not working. I have tried on my own for some time now. I was wondering if either of you have a spare moment this week, if I could stop by your lab with my Macbook to get this downloaded with the original version, i.e. blue = negative and red=positive.

Thanks very much

Amir

---

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/25

[mlinderm]

Do you have any error messages or other indications that might help us figure out why it is not working?

Note that you can always download the most recent "stock" plugin from: https://github.com/nolanlab/spade/blob/master/inst/tools/CytoSPADE.jar

Just drop the above file in the plugins directory of your Cytoscape installation.

[horowitzamir]

Hi Michael,

Somehow your message got lost in the string of other emails. I am just now trying to run SPADE again after using this latest cytoSPADE.jar file that you provided the link for. I will save the error messages if i can and bring them along with me.

Thanks very much again. Look forward to meeting you today.

All my best

Amir

_____ Amir Horowitz, PhD Postdoctoral Fellow / Department of Structural Biology / Parham Laboratory / Stanford University School of Medicine Fairchild Bldg / Room D100 / 299 Campus Drive West / Stanford, CA 94305-5126 ----- Original Message ----- From: "Michael Linderman" reply@reply.github.com To: "horowitzamir" amirh@stanford.edu Sent: Wednesday, January 18, 2012 6:09:03 PM Subject: Re: [spade] SPADE is not working (#25)

Do you have any error messages or other indications that might help us figure out why it is not working?

Note that you can always download the most recent "stock" plugin from: https://github.com/nolanlab/spade/blob/master/inst/tools/CytoSPADE.jar

Just drop the above file in the plugins directory of your Cytoscape installation.

---

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/25#issuecomment-3556871

[horowitzamir]

Dear Michael and Erin,

Hope this finds you both well. Erin, hope your time off has been relaxing. We had a brief discussion a while back regarding SPADE not having gating capabilities. Erin, you had mentioned how this was NOT a trivial task as you had to essentially re-write flow-jo within SPADE. You had also mentioned, however, that 'people' were working on this feature. I was wondering if this ever happened.

I was also hoping to ask either/both of you if you have ever run the program many times in a row for a dataset on purified cells, i.e. T cells (CD3), B cells (CD19), etc.? I am beginning to understand the consequence of running an 'unsupervised' approach, whereby in certain runs, rare populations may or may not be singled out as unique clusters. Peter's lab is in the process of assembling a very powerful computer/server and I am contemplating doing this for NK cells. I was hoping to get some feedback on this idea, i.e. if there is something that i should be expecting that would help in my interpretation of the data.

Thanks very much

All my best Amir

_____ Amir Horowitz, PhD Postdoctoral Fellow / Departments of Structural Biology and Microbiology & Immunology / Parham Laboratory / Stanford University School of Medicine / Fairchild Bldg / Room D100 / 299 Campus Drive West / Stanford, CA 94305-5126 ----- Original Message -----