Open birnbera opened 4 years ago
When running the software on my SWATH data I have encountered an error due to memory exhaustion as well as a warning regarding
centWave
(see below). Besides increasing the amount of memory available (i.e. running it on a cluster), are there some settings I should adjust to reduce some of the "background", e.g. the signal-to-noise or bandwidth parameters? Or any filters I should apply during conversion tomzXML
?
I am sorry for the late reply.
Regarding the warning from
centWave
, which I believe is used byxcms
, is there some other way that I should be converting mywiff
files intomzXML
besides the default options frommsConvert
? Or is this safe to ignore? I'm working more on the data analysis side than the data collection side, so I'm not sure if this is an issue with how the data was collected or if the conversion needs some specific options to generate a centroidedmzXML
file.
Yes, the 'centWave' method is used for peak detection and here we only support the converted centroid data other than the raw data (like 'wiff', etc.). To obtain the centroid data, one should add the 'peak picking' parameter when converting the raw data to 'mzXML' with msConvert.
Also, as an aside, it looks like the package is changing the working directory rather than reading from the specified input directory and using the supplied input directory for all read/write operations. This causes the
DecoMetDIA
function to fail since it can't find the files after changing directories:
Yes, the DecoMetDIA changes working directory when processing the data and change it back to the original one after the data are processed. However, the directory can not be changed back when error occurs, which should be corrected maybe. Some of the loaded packages are required in DecoMetDIA, while others may be induced by the required packages, such as xcms/CAMERA, etc. It's true that the loaded packages may overwriting other methods, which there is still no solutions to prevent this.
Hello, thanks for making this package. It looks very promising and is quite easy to read (a true accomplishment for R software!).
I am just beginning to test it with some of my data and I've run into a couple of issues that I would like some help with.
When running the software on my SWATH data I have encountered an error due to memory exhaustion as well as a warning regarding
centWave
(see below). Besides increasing the amount of memory available (i.e. running it on a cluster), are there some settings I should adjust to reduce some of the "background", e.g. the signal-to-noise or bandwidth parameters? Or any filters I should apply during conversion tomzXML
?Regarding the warning from
centWave
, which I believe is used byxcms
, is there some other way that I should be converting mywiff
files intomzXML
besides the default options frommsConvert
? Or is this safe to ignore? I'm working more on the data analysis side than the data collection side, so I'm not sure if this is an issue with how the data was collected or if the conversion needs some specific options to generate a centroidedmzXML
file.Also, as an aside, it looks like the package is changing the working directory rather than reading from the specified input directory and using the supplied input directory for all read/write operations. This causes the
DecoMetDIA
function to fail since it can't find the files after changing directories:Another aside, it seems that the package is exporting several of the libraries that it uses into the user's namespace, thus overwriting functions, etc. This is fine for command line use, but is a bit annoying when using the package as a library within other software.