Got an error when run "Check the classifier" part

[Xin Yi]

Hi Hannah,

    I am using garnett to analyze data with cicero output "gene activities score". The reference was TAIR10, and I didn't find any suitable db in the recommended website, so I didn't use any database as db(). When I doing the "Check the classifier" part, I got this error:

> marker_check <- check_markers(pbmc_cds, marker_file_path,

+                               db='none')

'arker file error. Illegal character '

Error in self$errorfunc(errtoken) : 

' at or near line number 1x error '

    I also tried to add the command " cds_gene_id_type = "SYMBOL",marker_file_gene_id_type = "SYMBOL"  " to the check_markers function but got the same error.My data loading with cicero_gene_activities.mtx and constructing a marker file looks just fine, so I am confused with this error. Could you tell me what's the cause of this error？

    Besides, my fdata didn't have "num_cells_expressed" column, and my pdata didn't have "FACS_type" column, because I didn't know the cell type yet. Will these conditions be the cause of that error?

    Thanks a lot for your help in advance!

Yixin

[Hannah Pliner]

Hi Yixin,

What does your "marker_file_path" look like? This error should have to do with the marker file itself - are there any strange characters in your marker file?

Best,

Hannah

[Xin Yi]

Hi Hannah,

    Thanks for your remind. Actually,yeah. I used a file editor software and found out that the file had an extra '\r' just before '\n', so it went wrong. After delete it, it worked!

    Thanks again~

Yi Xin

在 2019年9月12日星期四 UTC+8上午1:25:44，Hannah Pliner写道：