RnBeads error during rnb.run.differential

[Adrian Stankiewicz]

Dear all,

I'm trying to run differential analysis in RnBeads (command "D_result <- rnb.run.differential(I_result$rnb.set, report_dir)" - its located on the line 92 in the script I use: https://github.com/AdrianS85/varia/blob/master/R_RRBS.R; here is the sample sheet: https://github.com/AdrianS85/varia/blob/master/sample_annotationL.csv).

During step "STARTED Adding tables" I get such error:

Error in data.frame(..., check.names = FALSE) :
arguments imply differing number of rows 157853, 149960

Please see the traceback at https://github.com/AdrianS85/varia/blob/master/RnBeads_diff_error_traceback

The problem is similar to previously reported here https://www.biostars.org/p/293966/

I have successfully analyzed another batch of data (pre-processed using the same pipeline) with this script.

I would be very thankful for help. In case I missed some important information in my post, I apologize and please let me know.

Best,
Adrian

[Fabian]

Hi Adrian,

The problem you describe occurs sometimes when the disk-based files that we use to store the (differential) methylation data (using the ff package) are corrupted. In our experience this happens sometimes, e.g. when the I/O on the filesystem is high. Typically rerunning the analysis helps in resolving this issue. Hope that helps.

Best,

Fabian

[Adrian Stankiewicz]

Dear Fabian,

Indeed, this is the solution to the issue. Thank You very much!

Best,

Adrian