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HelenaLC / CATALYST

Cytometry dATa anALYsis Tools
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Error in GetChannels(fsom, colsToUse) #328

Closed klutzzzOOyyyq closed 1 year ago

klutzzzOOyyyq commented 1 year ago

hello , there is an error when I run cluster, I found the same error as issue 289, but it didn't solved. when I run : sce <- cluster(sce, features = "type",+xdim = 10, ydim = 10, maxK = 20, seed = 1234) it shows: o running FlowSOM clustering... Error in GetChannels(fsom, colsToUse) : Marker ^\QSIRPα (CD172a)\E$ could not be found

i have checked my panel, there is SIRPα (CD172a),but I don't know why there is \Q before and \E after. thank you very much

SamGG commented 1 year ago

Hi, \Q and \E are computer tags for matching marker names. α is not the same as a there is space after α These slight differences could explain the error.

klutzzzOOyyyq commented 1 year ago

Hi, \Q and \E are computer tags for matching marker names. α is not the same as a there is space after α These slight differences could explain the error.

sorry ,in my panel that is α not a, so the problem is still there ... In fact, my data is SIRPα (CD172a), which is alpha，but the program is still reporting an error

HelenaLC commented 1 year ago

Could you perhaps post your panel data.frame here (prior to running prepData(...)), and the rowData(sce)? This is more of a read.FCS/excel issue than CATAYST-specific, i.e., something's off with how the channel names are being read in.

klutzzzOOyyyq commented 1 year ago

Could you perhaps post your panel data.frame here (prior to running prepData(...)), and the rowData(sce)? This is more of a read.FCS/excel issue than CATAYST-specific, i.e., something's off with how the channel names are being read in.

i change the alpha into "a" in panel, then it works. thank you~