FCS to CSV

[Joan Slonczewski]

I tried converting an FCS file to CSV using your module.

It worked the first time (yesterday) but then did not work again today.

How might this be fixed?

Joan L. Slonczewski (they/them/theirs)
Professor of Biology
202 N. College Road
Kenyon College
Gambier, OH 43022
http://biology.kenyon.edu/slonc/slonc.htm
slonc...@kenyon.edu
Phone: 740-427-5397
Text: 740-504-2215

[Ted Liefeld]

Hi,

can you give us the job numbers for both Jobs and we will take a look at what happened.

Thanks

Ted

[Joan Slonczewski]

The job that worked was 455591.

Then I tried three times on a different file, jobs 456017, 456018, 456021. They did not work.

--
You received this message because you are subscribed to a topic in the Google Groups "GenePattern Help Forum" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/genepattern-help/7sKfm3bbb3o/unsubscribe.
To unsubscribe from this group and all its topics, send an email to genepattern-he...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/genepattern-help/887e2343-4c39-4217-a286-565f13b0d777n%40googlegroups.com.

[Ted Liefeld]

Hi

the problem appears to be the double spaces between the "Ph" and the "f" right at the start of the input filename,  and the logic that uses the base of the input filename for the output files is not working properly for that.

There are two quick workarounds;

1. Edit the input file name to remove the double spaces (ideally all spaces to be safe) and then re-run.

or

2. Change the value for the parameters "Output CSV file name" and "Output keyword file name" to not use the <Input.FCS.data.file_basename> placeholder.

Please let me know if this works for you

Ted

[Joan Slonczewski]

Thanks, Ted, changing the filename worked.

May I ask briefly what does it mean "convert channel to scale"?  I just want to be sure we are using the correct selection.

Joan

To view this discussion on the web visit https://groups.google.com/d/msgid/genepattern-help/42bb4af1-9c7c-43c1-a88e-63f695914f7en%40googlegroups.com.

[Ted Liefeld]

Joan,

The module doc says: 

===============

Specify whether to convert log channel values to linear scale or not:
              • true=convert channel to linear scale  (default)
               • no=no conversion, store same as in the FCS file 

===============

I am afraid that since the modules were developed at the BC Cancer Research Center we don't have anyone on the team that can answer with any more detail.  The author of the module is listed in the doc as Josef Spidlen (jspi...@bccrc.ca) so you could try contacting him.

Hope this helps

Ted

[Joan Slonczewski]

Thanks, Ted. The files do look correct, consistent with the BD software. I really appreciate your help.

Joan

To view this discussion on the web visit https://groups.google.com/d/msgid/genepattern-help/e0aa9c0c-0851-4f84-8807-ab26329143ben%40googlegroups.com.

[Ted Liefeld]

I am glad that things are working for you now.  Let us know if you have any other questions

Ted

You received this message because you are subscribed to the Google Groups "GenePattern Help Forum" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genepattern-he...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/genepattern-help/CAAzKrdJ2LoMME2kHx3BJKQpAHxQ1jbfm5nqyU2zMLieBc-7c0A%40mail.gmail.com.

--

Ted Liefeld                                      UC San Diego

Mesirov Lab                                    lie...@ucsd.edu                                
Office 2A24, BRF-II                        858-246-1974