Sce2FCS prevent renaming of channels

[ammasakshay]

trafficstars

fs <- sce2fcs(sce, split_by = "sample_id")

      orig_channel_name new_channel_name
$P7N               CD45           CD45-1
$P9N               CD45           CD45-2
$P11N              CD45           CD45-3
$P12N              CD45           CD45-4
$P13N              CD45           CD45-5
$P21N                EQ             EQ-1
$P23N                EQ             EQ-2
$P58N                EQ             EQ-3

Can we prevent it from automatically renaming channels?

[ammasakshay]

Got it, thanks. I think I see the issue now.

What's happening is that Im normalizing 8 runs of the experiment together. I then write them to .fcs files using the sce2fcs function. I then take each run and de-barcode each run individually. However because channel names get changed during this process, during the debarcoding I get the error:

Error in assignPrelim(sce, mat) : Couldn't match masses extracted from channel names and debarcoding scheme.

I'm not quite sure how to fix this.

On Thu, Apr 1, 2021 at 1:43 PM Helena L. Crowell @.***> wrote:

Unfortunately not, because rownames in the SCE have to be unique...

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