Regarding DeepRTAlign, I have three questions #2
Description
① I found that when the number of peaks in the Peaklist is relatively small (around 60), the information_all.csv file is generated correctly, but the information_target.csv file is not, resulting in the following error:
FileNotFoundError: [Errno 2] No such file or directory: 'mass_align_all_information/information_target.csv'
Additionally, when I set FDR=1, the information_target.csv file is still not generated.
When I run the process with files averaging 10,000 peaks, everything works fine, and the resulting information_target.csv contains only about 2,000 features. It seems that this alignment process significantly reduces the number of final features compared to workflows like XCMS. Is that correct?
② Can I use a peak-picking tool along with DeepRTAlign to obtain the final peak list for general upstream analysis, or do I need to perform additional 【peak grouping】 after using DeepRTAlign?
③I noticed that the final result, information_target.csv, is a table with repeated features integrated vertically across different samples. Should this table be transformed to get an output containing peak values across different samples, which can then be used as the final upstream table?