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cbielow / PTXQC

A Quality Control (QC) pipeline for Proteomics (PTX) results generated by MaxQuant
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Quitting from R template and can't generate template file #115

Open yuha6189 opened 2 years ago

yuha6189 commented 2 years ago

Dear Chris, I have used PTXQC (v. 1.0.12 ) and it has been working great. However, I recently ran a MaxQuant analysis with a few default output files selected: msmsScans.txt, ms3Scans.txt, mzRange.txt, passeMsmsScans.txt, and accumulatedMsmsScans.txt. To accommodate this change, I changed the order value for MSMS scans (and even MSMS) metrics in the yaml file (attached) and manually assigned the yaml file to createReport function, however, I keep getting this error msg below. I couldn't figure out what caused the error and any help will be greatly appreciated! I've attached my R script and yaml file(both converted to txt for uploading). Thanks!!

"Quitting from lines 187-223 (PTXQC_report_template.Rmd) Error in seq_len(n) : argument must be coercible to non-negative integer In addition: Warning messages: 1: Vectorized input to element_text() is not officially supported. Results may be unexpected or may change in future versions of ggplot2. 2: Removed 60 rows containing missing values (position_stack). 3: In max(f) : no non-missing arguments to max; returning -Inf

(https://github.com/cbielow/PTXQC/files/7766827/report_v1.0.12_2075A.yaml.txt) e.txt](https://github.com/cbielow/PTXQC/files/7766821/R_code.txt) "

cbielow commented 10 months ago

hi, you post got totally swamped by x-mas. Apologies for not following up. I tried to reproduce the issue using your .yaml file and code, but both v1.0.12 and the current PTXQC work fine when I run them on a single msmsScans.txt (the other files you mentioned, like mzRange.txt, are not used by PTXQC).

So, if still relevant, please upload the txt folder somewhere and I can take a look. It must be something special in your data which is causing this.