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kroganlab / mist

mist R package files
GNU General Public License v3.0
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Error in if (length(baits_to_exclude) #20

Closed vinayduggi closed 2 years ago

vinayduggi commented 2 years ago

Hi, I am trying to run the MIST algorithm on my affinity proteomics data. I think I have everything in the right format etc. Upon running the first phase - preprocessing with data.txt and keys.txt files only

LOADING DEPENDENCIES... Warning message: package ‘ggplot2’ was built under R version 4.1.1 All required R libraries accounted for. PREPROCESSING FILES READING FILES !!! CHARACTERS FOUND IN unique_pep COLUMN. CONVERTING TO NUMERIC. FILTERING COMMON CONTAMINANTS FILTERED 529 CONTAMINANTS MERGING KEYS WITH DATA 98 TOTAL BAITS DETECTED 98/98 BAITS DETECTED IN DATA FILE 98/98 BAITS DETECTED IN KEYS FILE CONVERTING TO MATRIX COLLAPSE FILE IS EMPTY Remove file is empty EXCLUSIONS FILE IS EMPTY QUALITY CONTROL Saving 7 x 7 in image MIST Error in if (length(baits_to_exclude) == 0 & sum(rowSums(abundance)) > : missing value where TRUE/FALSE needed Calls: main ... mist.main -> mist.getMetrics -> mist.getSpecificity Execution halted

I can't work out what's wrong. From google searches of similar error messages, I think it may be something to do with some parameters, but I'm unsure which line (in which script) I need to modify. Any ideas? Regards, Vinay

vinayduggi commented 2 years ago

@jvondollen ......Can you please reply to this