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This is a R package for alignment of DIA mass-spec data
Hi,
a new problem has appeared. I always get the message:
Error in (function (classes, fdef, mtable) :
cannot find inherited method for function 'dbGetQuery' for signature '"mzRpwiz", "character"'.
Geting global alignment of run6 and run12,Increasing maxFdrGlobal 10 times
n = 10
The execution time for calculating global alignment:
Time difference of 0.3936419 secs
Performing reference-based alignment.
Processing Batch 1
Error in (function (classes, fdef, mtable) :
cannot find inherited method for function 'dbGetQuery' for signature '"mzRpwiz", "character"'.
Sorry for all the questions, however I am not very familiar with R... . Is this error message due to me?
Many greetings
Is it possible to change the assumed chromatogram files folder to something more general? Like xics or chromatograms? Because I usually store my sqMass files in a folder called sqmass, not mzml since they're not mzML files, which causes an issue with get_filenames.R#L84.
It's not a problem to just rename the folder to mzml, more so just a personal preference..
getLOESSfit
returns an uninformative error when using non-optimal maxGlobalFdr for loess fit.
Error in vecseq(f__, len__, if (allow.cartesian || notjoin || !anyDuplicated(f__, :
Join results in 5359 rows; more than 5228 = nrow(x)+nrow(i). Check for duplicate key values in i each of which join to the same group in x over and over again. If that's ok, try by=.EACHI to run j for each group to avoid the large allocation. If you are sure you wish to proceed, rerun with allow.cartesian=TRUE. Otherwise, please search for this error message in the FAQ, Wiki, Stack Overflow and data.table issue tracker for advice.
There is a check that increments the maxGlobalFdr by 10 times get_global_fit.R#L246, but in my case I had to decrease the FDR to 0.01 for one run pair, and even further 0.006 for another run pair. Might need to implement another check that decrements maxGlobalFdr.
Whether MRM data is supported now?
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