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)
"
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)
"