markers not included in single cell element by preData function

[SchellB]

Hello,

I am struggling with an issue on CATALYST. It seems that some markers have not been included in the single cell element created by prepData function. Here is my code: sce <- prepData(result, panel, md, panel_cols=list(channel="channel", antigen="antigen", class="marker_class"), md_cols = list(file = "file_name", id = "sample_id", factors =c("condition", "cell_id")))

colnames(result) [1] "FSC-A" "FSC-H" "SSC-A" "SSC-B-A"
[5] "SSC-B-H" "SSC-H" "FJComp-APC-Vio 770-A" "FJComp-Alexa Fluor 647-A" [9] "FJComp-Alexa Fluor 700-A" "FJComp-BB515-A" "FJComp-BUV395-A" "FJComp-BUV563-A"
[13] "FJComp-BUV615-A" "FJComp-BUV661-A" "FJComp-BUV737-A" "FJComp-BUV805-A"
[17] "FJComp-BV421-A" "FJComp-BV605-A" "FJComp-BV650-A" "FJComp-BV711-A"
[21] "FJComp-BV786-A" "FJComp-PE-A" "FJComp-PE-Cy7-A" "FJComp-PE-Dazzle594-A"
[25] "FJComp-Pacific Blue-A" "FJComp-PerCP-Cy5.5-A" "FJComp-PerCP-eFluor 710-A" "FJComp-eFluor 506-A"
[29] "Time"

panel$channel [1] "FSC-A" "FSC-H" "SSC-A" "SSC-B-A"
[5] "SSC-B-H" "SSC-H" "FJComp-APC-Vio 770-A" "FJComp-Alexa Fluor 647-A" [9] "FJComp-Alexa Fluor 700-A" "FJComp-BB515-A" "FJComp-BUV395-A" "FJComp-BUV563-A"
[13] "FJComp-BUV615-A" "FJComp-BUV661-A" "FJComp-BUV737-A" "FJComp-BUV805-A"
[17] "FJComp-BV421-A" "FJComp-BV605-A" "FJComp-BV650-A" "FJComp-BV711-A"
[21] "FJComp-BV786-A" "FJComp-PE-A" "FJComp-PE-Cy7-A" "FJComp-PE-Dazzle594-A"
[25] "FJComp-Pacific Blue-A" "FJComp-PerCP-Cy5.5-A" "FJComp-PerCP-eFluor 710-A" "FJComp-eFluor 506-A"
[29] "Time"

all(panel$channel %in% colnames(result)) [1] TRUE

And yet the sce displays:

sce@rowRanges@elementMetadata@listData[["channel_name"]] [1] "FJComp-APC-Vio 770-A" "FJComp-Alexa Fluor 647-A" "FJComp-Alexa Fluor 700-A" "FJComp-BB515-A"
[5] "FJComp-BUV395-A" "FJComp-BUV563-A" "FJComp-BUV615-A" "FJComp-BUV661-A"
[9] "FJComp-BUV737-A" "FJComp-BUV805-A" "FJComp-BV421-A" "FJComp-BV605-A"
[13] "FJComp-BV650-A" "FJComp-BV711-A" "FJComp-BV786-A" "FJComp-PE-Cy7-A"
[17] "FJComp-PE-Dazzle594-A" "FJComp-PerCP-Cy5.5-A" "FJComp-PerCP-eFluor 710-A" "FJComp-eFluor 506-A"

What happened to the other channels ?

Thank you for your help.

Berenice

[SchellB]

I just realized now, I havn't set the parameter FACS to TRUE. All is solved now. Sorry for the trouble.

[SchellB]

I just realized now, I havn't set the parameter FACS to TRUE. All is solved now. Sorry for the trouble.