search

shuzhao-li-lab / asari

asari, metabolomics data preprocessing
Other
37 stars 9 forks source link

documentation comments of `workflow.process_project()` #91

Open NchuYJ opened 1 month ago

NchuYJ commented 1 month ago

asari.workflow.process_project() the function documentation comments hints it takes centroid MS data for batch processing, however, the function single_sample_EICs_ do this job uses pymzml.run.Reader(), which do not convert. Is this a mistake ?

image

jmmitc06 commented 1 month ago

The conversion to centroided data should be done before processing with asari. For instance, during the conversion from the vendor specific format to mzML.

Does this answer your question?

May 28, 2024 10:11:46 AM NchuYJ @.***>:

asari.workflow.process_project() the function documentation comments hints it takes centroid MS data for batch processing, however, the function single_sampleEICs do this job uses pymzml.run.Reader(), which do not convert. Is this a mistake ?

image.png (view on web)[https://github.com/shuzhao-li-lab/asari/assets/83570131/1453f6bf-5900-47f3-ba94-d923ef22f5ce]

— Reply to this email directly, view it on GitHub[https://github.com/shuzhao-li-lab/asari/issues/91], or unsubscribe[https://github.com/notifications/unsubscribe-auth/ACNJZYMUULXGL7JL43WEILLZESGCFAVCNFSM6AAAAABINA3PGWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGMZDCMJYGY4DQMI]. You are receiving this because you are subscribed to this thread. [Tracking image][https://github.com/notifications/beacon/ACNJZYJPYSQAJFBOWJKHCQLZESGCFA5CNFSM6AAAAABINA3PGWWGG33NNVSW45C7OR4XAZNFJFZXG5LFVJRW63LNMVXHIX3JMTHIUWUAIE.gif]

NchuYJ commented 1 month ago

Hi Shuzhao-Li-Lab/Asari,

Thanks you for the answer, now it is clear.

On Wed, May 29, 2024 at 1:03 AM Joshua Mitchell @.***> wrote:

The conversion to centroided data should be done before processing with asari. For instance, during the conversion from the vendor specific format to mzML.

Does this answer your question?

May 28, 2024 10:11:46 AM NchuYJ @.***>:

asari.workflow.process_project() the function documentation comments hints it takes centroid MS data for batch processing, however, the function single_sampleEICs do this job uses pymzml.run.Reader(), which do not convert. Is this a mistake ?

image.png (view on web)[ https://github.com/shuzhao-li-lab/asari/assets/83570131/1453f6bf-5900-47f3-ba94-d923ef22f5ce]

— Reply to this email directly, view it on GitHub[ https://github.com/shuzhao-li-lab/asari/issues/91], or unsubscribe[ https://github.com/notifications/unsubscribe-auth/ACNJZYMUULXGL7JL43WEILLZESGCFAVCNFSM6AAAAABINA3PGWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGMZDCMJYGY4DQMI].

You are receiving this because you are subscribed to this thread. [Tracking image][ https://github.com/notifications/beacon/ACNJZYJPYSQAJFBOWJKHCQLZESGCFA5CNFSM6AAAAABINA3PGWWGG33NNVSW45C7OR4XAZNFJFZXG5LFVJRW63LNMVXHIX3JMTHIUWUAIE.gif]

— Reply to this email directly, view it on GitHub https://github.com/shuzhao-li-lab/asari/issues/91#issuecomment-2136243123, or unsubscribe https://github.com/notifications/unsubscribe-auth/AT5S3U5DSNBBE45WALF3553ZEUEL3AVCNFSM6AAAAABINA3PGWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMZWGI2DGMJSGM . You are receiving this because you authored the thread.Message ID: @.***>