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Catalyst Pre-Processed file in Cytobank

PostPosted: Thu Jun 21, 2018 7:54 pm
by CRStevens
Hi All,

I've been playing around with the CATALYST package in R and was wondering if anyone else has had an issue with uploading the concatenated/normalized/debarcoded fcs files onto Cytobank? It seems as there are two of every keyword in my FCS Header Text and Cytobank picks the earliest one. This doesn't seem like an issue, except it chooses total events from the master file (say 1 million events) but the individual debarcoded file is only 200k events. This makes the files unusable in Cytobank as they see a discrepancy in event numbers and the $TOT keyword. Any help with this would be much appreciated!

-Chad

Re: Catalyst Pre-Processed file in Cytobank

PostPosted: Sun Jun 24, 2018 8:28 pm
by schevrie
Dear Chad,

I just tried again the pre-processing pipeline of CATALYST using the version 1.5.2 of the R package as you described it (concat, normalization, debarcoding) and I didn't experience any issue upon uploading into Cytobank. Every debarcoded file was displayed correctly. Can you let me know which issue you are facing in Cytobank? the files cannot be opened at all ? Can you also specify which version of Catalyst you are using?

Best

St├ęphane

Re: Catalyst Pre-Processed file in Cytobank

PostPosted: Mon Jun 25, 2018 6:52 am
by markrobinsonca
Dear Chad,

I guess it would also be helpful to know what version of 'flowCore' you have, which is where the code to write objects to FCS files resides. Could you post the output of the following three commands:

library(CATALYST)
library(flowCore)
sessionInfo()

?

Thanks, Mark

Re: Catalyst Pre-Processed file in Cytobank

PostPosted: Mon Jun 25, 2018 3:08 pm
by CRStevens
Thank you all or your replies. Attached is the requested output.

sessioninfo.PNG



Also this shows the FCS Header for the file on Cytobank. You can see that there are 4 $TOT keywords in the file and it is reading in the number of events from the original concatenated FCS and not from the debarcoded $TOT.


FCS raw header from cytobank.PNG
FCS raw header from cytobank.PNG (7.04 KiB) Viewed 4122 times



Also of note, in R, I can locate the $TOT for each debarcoded file by using the command line, so I know the right keyword is there, but Cytobank gets confused and looks at the earliest one.

file before upload _Flowcore.PNG
file before upload _Flowcore.PNG (4.13 KiB) Viewed 4122 times


-Chad