Open OlivierLangella opened 1 month ago
thanks, we should definitely make this work. Is it normal that there are no values in the FDR fields?
Hello @mlocardpaulet ! oh no, that's a bug... thanks I'll check this
I've checked the file, here are the FDR fields reported :
i2m_psm_fdr_threshold_target 0.006
peptide_fdr 0.008561447245
protein_fdr 0.009234643907
psm_fdr 0.005999419143
is this the right fields or is there an other field ? https://github.com/Proteobench/ProteoBench/blob/369dd02231560e3d5be7c624d06ebf3bb45b6484/proteobench/io/params/i2masschroq.py#L33
Hello @mlocardpaulet , is this field OK or am I missing something ? Thank you Olivier
yes, these are OK :). It is just that these are empty in the parameter file in the cloud.
Oh that is weird, when I download the file in the cloud, I get this :
langella@piccolo:~/Téléchargements$ cat /tmp/Project\ parameters.tsv | grep fdr
i2m_psm_fdr_threshold_target 0.006
peptide_fdr 0.008561447245
protein_fdr 0.009234643907
psm_fdr 0.005999419143
in the directory "i2m_and_sage". Tell me if it is the case for you, otherwise I'll just put the file elsewhere.
Thanks again Olivier
Oh that is weird, when I download the file in the cloud, I get this :
langella@piccolo:~/Téléchargements$ cat /tmp/Project\ parameters.tsv | grep fdr i2m_psm_fdr_threshold_target 0.006 peptide_fdr 0.008561447245 protein_fdr 0.009234643907 psm_fdr 0.005999419143
in the directory "i2m_and_sage". Tell me if it is the case for you, otherwise I'll just put the file elsewhere.
Thanks again Olivier
Oh no! You are right. Sorry. I don't know what I did to not see these 🤦 It looks all good. Sorry for the wasted time.
Is your feature request related to a problem? Please describe. no problem, many thanks for the new web user interface ! it is well done. i2MassChroQ is already supported, but I had to add new parameters in the metadata specific to the Sage identification engine. Those new tags in the metadata csv file are not taken into account yet.
Describe the solution you'd like So I've reported the main Sage parameters in the metadata file. The new parameters dedicated to sage are present in this file :
in the dedicated cloud.
Additional context The result is interesting and I would like to publish it with relevant metadata
Thanks a lot ! Olivier