[Bug]: lack information on sex chromosomes

SunYidan2021 commented 1 month ago

Contact Details

No response

Scripts

01-check_data.sh

What happened?

We don't genotyped data on sex chromosomes and the probes on sex chromosomes were excluded in previous QC steps. Is it possiable to continue to analysis when the ERROR occured?

 The following errors were encountered, and must be addressed before continuing:
- fewer than 80% chrx and chry probes. Please include chrx and y probes

How can the bug be reproduced?

No response

R version

4.2.1 (June, 2022)

Python version

None

Relevant log output

No response

epzjlm commented 3 weeks ago

Hello, See some more info on chromosome X and Y here: https://github.com/genetics-of-dna-methylation-consortium/godmc_phase2/wiki/chromosome-X

If you don't have any chromosome X or Y in your methylation data then you can ignore this message.

SunYidan2021 commented 2 weeks ago

Hello, See some more info on chromosome X and Y here: https://github.com/genetics-of-dna-methylation-consortium/godmc_phase2/wiki/chromosome-X

If you don't have any chromosome X or Y in your methylation data then you can ignore this message.

Hello, if I understand correctly, I can still work on module 08 which need QC 03f. However, I got an error as following:

Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
Calls: load -> readChar
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file '~/GoDMC/data/processed_data/methylation_data/untransformed_methylation_adjusted_pcs.Male.chrX.RData', probable reason 'No such file or directory'
Execution halted

Should I also skip module 08?

genetics-of-dna-methylation-consortium / godmc_phase2