QingfeiPan
commented
1 month ago Hi ,I'm new to SJARACNe , aftering using downsample to run SJARACNe ,I get consensus_networkncol.txt files seperately in TF/SIG，I decided to calculate driver activities with getActivity_individual() , however some error appeared.
But I have checked that sampleNames of assayData and phenoData are the same and validObject()returns TRUE.
my code is : generateSJARACNeInput(input_eset = day7_log2cpm.eset, group_name = "leiden",sjaracne_dir = "./my_path/SJARACNe",species_type = "mm", driver_type = "TF_SIG", downSample_N = 1000)
sjaracne local -e /my_path/day7_Network/SJARACNe/cluster0/cluster0.8154_1000.exp.txt -g /my_path/day7_Network/SJARACNe/cluster0/TF/cluster0.730_1000.tf.txt -o /my_path/day7_Network/SJARACNe/cluster0/TF -n 100 -pc 1e-2 -pb 1e-5 -tmp ./tmp/
activity_cluster0.eset <- getActivity_individual(input_eset = cluster0_day7_log2cpm.eset,network_file.tf = "./SJARACNe/cluster0/TF/consensus_networkncol.txt",network_file.sig = "./SJARACNe/cluster0/SIG/consensus_networkncol.txt",driver_type = "TF_SIG")
Does anyone have ideas about the source of the error? Thanks a lot !!
Hi @karlie002 ,
Thanks for your feedback!
We met this error once before, and the reason turned out to be that some symbols in the column names, "-" in that case, were automatically converted to dot (".") during the activity calculation, since by default R doesn't accept "-" in the column names of the data frame. Now we have fixed this error. Would you please reinstall the scMINER R package and try the function getActivity_individual() again?
Best, Qingfei
karlie002
Hi ,I'm new to SJARACNe , aftering using downsample to run SJARACNe ,I get consensus_networkncol.txt files seperately in TF/SIG，I decided to calculate driver activities with getActivity_individual() , however some error appeared.
But I have checked that sampleNames of assayData and phenoData are the same and validObject()returns TRUE.
my code is : generateSJARACNeInput(input_eset = day7_log2cpm.eset, group_name = "leiden",sjaracne_dir = "./my_path/SJARACNe",species_type = "mm", driver_type = "TF_SIG", downSample_N = 1000)
sjaracne local -e /my_path/day7_Network/SJARACNe/cluster0/cluster0.8154_1000.exp.txt -g /my_path/day7_Network/SJARACNe/cluster0/TF/cluster0.730_1000.tf.txt -o /my_path/day7_Network/SJARACNe/cluster0/TF -n 100 -pc 1e-2 -pb 1e-5 -tmp ./tmp/
activity_cluster0.eset <- getActivity_individual(input_eset = cluster0_day7_log2cpm.eset,network_file.tf = "./SJARACNe/cluster0/TF/consensus_networkncol.txt",network_file.sig = "./SJARACNe/cluster0/SIG/consensus_networkncol.txt",driver_type = "TF_SIG")
Does anyone have ideas about the source of the error ? Thanks a lot !!