Fwd: Galaxy default parameters

[Curtis Huttenhower]

Hi Patricia - many thanks for getting in touch, and I'm forwarding this along to the MaAsLin users group to help out. I know the first answer offhand, inasmuch as 0.0001 is in relative abundance units rather than percent (so it's equal to 0.01%), but I'm not sure myself about the second Galaxy question (George / others?)

Thanks again -

Curtis

---------- Forwarded message ---------
From: Patricia Rojas <P.R...@bham.ac.uk>
Date: Tue, Nov 5, 2019 at 6:46 AM
Subject: Galaxy default parameters
To: Huttenhower, Curtis <chut...@hsph.harvard.edu>

Dear team, 

My name is Patricia Rojas , and  first of all congratulation for you amazing job with MaAsLin! 

I have some doubt about the parameters in Galaxy, so I hope you could help me with them. 

1) Considering that my  bacterial matrix has proportional data ranging from 0 to 1.0, for the default parameter  "Minimum for feature relative abundance filtering = 0.0001", does it means that the  minimum percentage relative abundance is 0.01% or is it already in %?? 

2) Is MaAsLin in Galaxy considering any maximum percentage of samples with missing metadata? Or should I do this filtering before? 

Thank you very much in advance, 

All the best, 

Patricia 

Patricia Rojas-Sánchez, PhD.
Research fellow
Institute of Applied Health Research & ITM
University of Birmingham

Phone: +44 7727 180108

[Mallick, Himel]

Hi Patricia – as far as I can tell, MaAsLin (or MaAsLin2) does not have a parameter that controls the maximum percentage of samples with missing metadata. It automatically removes the missing samples on a per-feature basis when doing the linear modeling, which means depending on which covariates (or metadata) you are including in your model, any row (sample) with missing data either in Y (feature) or X (design matrix) will be removed. I hope this answers your question.

 

Many thanks,

Himel

 

From: maasli...@googlegroups.com <maasli...@googlegroups.com> On Behalf Of Curtis Huttenhower
Sent: Wednesday, November 6, 2019 4:34 PM
To: maasli...@googlegroups.com
Cc: George Weingart <george....@gmail.com>; sagunma...@gmail.com; Ma, Siyuan <sim...@mail.harvard.edu>
Subject: Fwd: Galaxy default parameters

 

EXTERNAL EMAIL – Use caution with any links or file attachments.

--
You received this message because you are subscribed to the Google Groups "MaAsLin-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to maaslin-user...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/maaslin-users/CAComemZ_Y%3DuLqa5gQYp99dvRT-sxn3%2BC%2Be90YJFnVkoHBTHjag%40mail.gmail.com.

Notice:  This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth,
New Jersey, USA 07033), and/or its affiliates Direct contact information
for affiliates is available at
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from
your system.