Issues with MFAssignR #27
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Hello Angela,
That is definitely a strange situation. Would you be willing to share the
script you are using with me? Most likely there is something missing, but I
can't tell for sure without seeing it. Does it generate an error, or is it
just not assigning molecular formulas? If you can also let me know what
version of R, RStudio, and MFAssignR you are using as well that would be
helpful for diagnosing the issue.
Let me know if you have any other questions.
Thanks,
Simeon
…On Mon, Feb 20, 2023 at 11:16 AM AngelaDCP ***@***.***> wrote:
Hi,
thank you so much for this work! It is very helpful!
I'm trying to use MFAssignR for MS data assignment acquired on a FT-ICR.
When I run the script I can get the MFAssign for CHO, but then I don't get
any assignment when I run MFAssign with Heteroatoms.
I'm wondering if I'm missing something or I wrote something wrong in my
script.
Hopefully I can get some help!
Thank you,
best
Angela
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Dear Simeon, I'm getting this error and it will cause issues later when I run MFAssignCHO and MFAssign
Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: The following objects are masked from ‘package:base’: |
|
Hello Angela,
That error suggests that the loading of dplyr is masking some function in
the "stats" package, which is not explicitly used in MFAssignR and
shouldn't cause a problem directly. The objects masked from the "base"
package may cause an issue if they underpin some of the other functions
that I am using in MFAssignR, but I don't call them explicitly in any of
the functions.
In this case the biggest issue seems like it has to do with loading R and
the various packages on your computer, I have seen other users have issues
with getting aspects of this working on Macs before, though I don't know if
they had the same issues as you, and it definitely doesn't mean you are
doing anything wrong.
At the core of the issue I think is just not having the various version
agreeing with each other (R and MFAssignR in particular). I had to make
some changes to MFAssignR when a newer version of R came out a while back.
I am attaching the most up to date version of MFAssignR so you can try to
get it installed and see if it works any better for you. It is the same
version as is currently on Github, but sometimes it seems like people have
had issues getting it installed from the Github files.
I apologize for the slow response. If you could try to install this new
version of MFAssignR (it also may be worth trying to re-install R and
RStudio) and let me know what happens that would be good. If you continue
to have problems, please let me know and I will try to respond more
promptly.
Thanks,
Simeon
…On Thu, Mar 2, 2023 at 11:54 AM AngelaDCP ***@***.***> wrote:
Dear Simeon,
I'm using RStudio Version 2022.12.0+353 on a MacBookPro.
I'm getting this error and it will cause issues later when I run
MFAssignCHO and MFAssign
library(dplyr)
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
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Hi Simeon,
Sorry for my late reply.
I tried to fix the issues but I still have the same problem.
So then I used your .rmd file and it looks like it works ( at least I don't
get any error).
Now I have some problems with the assignment as I will get only 1 or 2
formulas assigned on a list of 144 signals . Any suggestions?
Thank you,
Angela
Il giorno gio 9 mar 2023 alle ore 11:21 Simeon Schum <
***@***.***> ha scritto:
… Hello Angela,
That error suggests that the loading of dplyr is masking some function in
the "stats" package, which is not explicitly used in MFAssignR and
shouldn't cause a problem directly. The objects masked from the "base"
package may cause an issue if they underpin some of the other functions
that I am using in MFAssignR, but I don't call them explicitly in any of
the functions.
In this case the biggest issue seems like it has to do with loading R and
the various packages on your computer, I have seen other users have issues
with getting aspects of this working on Macs before, though I don't know if
they had the same issues as you, and it definitely doesn't mean you are
doing anything wrong.
At the core of the issue I think is just not having the various version
agreeing with each other (R and MFAssignR in particular). I had to make
some changes to MFAssignR when a newer version of R came out a while back.
I am attaching the most up to date version of MFAssignR so you can try to
get it installed and see if it works any better for you. It is the same
version as is currently on Github, but sometimes it seems like people have
had issues getting it installed from the Github files.
I apologize for the slow response. If you could try to install this new
version of MFAssignR (it also may be worth trying to re-install R and
RStudio) and let me know what happens that would be good. If you continue
to have problems, please let me know and I will try to respond more
promptly.
Thanks,
Simeon
On Thu, Mar 2, 2023 at 11:54 AM AngelaDCP ***@***.***> wrote:
> Dear Simeon,
> I'm using RStudio Version 2022.12.0+353 on a MacBookPro.
>
> I'm getting this error and it will cause issues later when I run
> MFAssignCHO and MFAssign
>
> library(dplyr)
>
> Attaching package: ‘dplyr’
>
> The following objects are masked from ‘package:stats’:
>
> filter, lag
>
>
> The following objects are masked from ‘package:base’:
>
> intersect, setdiff, setequal, union
>
>
> —
> Reply to this email directly, view it on GitHub
> <#27 (comment)
>,
> or unsubscribe
> <
https://github.com/notifications/unsubscribe-auth/AF72HFDEEAWEOKYBND6PZG3W2DGC5ANCNFSM6AAAAAAVCCAL7E
>
> .
> You are receiving this because you commented.Message ID:
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Hello Angela,
I think the initial issue is that you were seeing the warnings that were
present in the code, but didn't actually make it not work properly. Someone
else had a similar issue and it was masked by my version of the .rmd
because I always turn warnings off. However, the issue that was causing
those warnings has been fixed, though I haven't updated GitHub because I
wanted to make sure there weren't any other issues caused by fixing it.
As for only two assignments out of 144, that could be an issue of no
formula extensions between the various compounds, thus making it harder to
assign formulas. I would recommend extending the DeNovo cutoff (assuming
you have masses beyond the default of 300 m/z and also turning "on" the
MSMS option if it is not already on. These are the two main things that can
improve coverage of assignment when dealing with a sparse data set. If you
still have issues I would be glad to take a look at the data if you are
willing to share it. If you want to email me directly you can use
***@***.***
Let me know if you have any other questions or need any clarification.
Thanks,
Simeon
…On Wed, Apr 12, 2023 at 7:38 AM AngelaDCP ***@***.***> wrote:
Hi Simeon,
Sorry for my late reply.
I tried to fix the issues but I still have the same problem.
So then I used your .rmd file and it looks like it works ( at least I don't
get any error).
Now I have some problems with the assignment as I will get only 1 or 2
formulas assigned on a list of 144 signals . Any suggestions?
Thank you,
Angela
Il giorno gio 9 mar 2023 alle ore 11:21 Simeon Schum <
***@***.***> ha scritto:
> Hello Angela,
>
> That error suggests that the loading of dplyr is masking some function in
> the "stats" package, which is not explicitly used in MFAssignR and
> shouldn't cause a problem directly. The objects masked from the "base"
> package may cause an issue if they underpin some of the other functions
> that I am using in MFAssignR, but I don't call them explicitly in any of
> the functions.
>
> In this case the biggest issue seems like it has to do with loading R and
> the various packages on your computer, I have seen other users have
issues
> with getting aspects of this working on Macs before, though I don't know
if
> they had the same issues as you, and it definitely doesn't mean you are
> doing anything wrong.
>
> At the core of the issue I think is just not having the various version
> agreeing with each other (R and MFAssignR in particular). I had to make
> some changes to MFAssignR when a newer version of R came out a while
back.
> I am attaching the most up to date version of MFAssignR so you can try to
> get it installed and see if it works any better for you. It is the same
> version as is currently on Github, but sometimes it seems like people
have
> had issues getting it installed from the Github files.
>
> I apologize for the slow response. If you could try to install this new
> version of MFAssignR (it also may be worth trying to re-install R and
> RStudio) and let me know what happens that would be good. If you continue
> to have problems, please let me know and I will try to respond more
> promptly.
>
> Thanks,
> Simeon
>
> On Thu, Mar 2, 2023 at 11:54 AM AngelaDCP ***@***.***> wrote:
>
> > Dear Simeon,
> > I'm using RStudio Version 2022.12.0+353 on a MacBookPro.
> >
> > I'm getting this error and it will cause issues later when I run
> > MFAssignCHO and MFAssign
> >
> > library(dplyr)
> >
> > Attaching package: ‘dplyr’
> >
> > The following objects are masked from ‘package:stats’:
> >
> > filter, lag
> >
> >
> > The following objects are masked from ‘package:base’:
> >
> > intersect, setdiff, setequal, union
> >
> >
> > —
> > Reply to this email directly, view it on GitHub
> > <
#27 (comment)
> >,
> > or unsubscribe
> > <
>
https://github.com/notifications/unsubscribe-auth/AF72HFDEEAWEOKYBND6PZG3W2DGC5ANCNFSM6AAAAAAVCCAL7E
> >
> > .
> > You are receiving this because you commented.Message ID:
> > ***@***.***>
> >
>
> —
> Reply to this email directly, view it on GitHub
> <#27 (comment)
>,
> or unsubscribe
> <
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>
> .
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>
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Thank you!
I sent you an email with my data. Let me know if you got it. ( better check
the spam folder) .
thanks,
Angela
Il giorno mer 12 apr 2023 alle ore 15:06 Simeon Schum <
***@***.***> ha scritto:
… Hello Angela,
I think the initial issue is that you were seeing the warnings that were
present in the code, but didn't actually make it not work properly. Someone
else had a similar issue and it was masked by my version of the .rmd
because I always turn warnings off. However, the issue that was causing
those warnings has been fixed, though I haven't updated GitHub because I
wanted to make sure there weren't any other issues caused by fixing it.
As for only two assignments out of 144, that could be an issue of no
formula extensions between the various compounds, thus making it harder to
assign formulas. I would recommend extending the DeNovo cutoff (assuming
you have masses beyond the default of 300 m/z and also turning "on" the
MSMS option if it is not already on. These are the two main things that can
improve coverage of assignment when dealing with a sparse data set. If you
still have issues I would be glad to take a look at the data if you are
willing to share it. If you want to email me directly you can use
***@***.***
Let me know if you have any other questions or need any clarification.
Thanks,
Simeon
On Wed, Apr 12, 2023 at 7:38 AM AngelaDCP ***@***.***> wrote:
> Hi Simeon,
> Sorry for my late reply.
>
> I tried to fix the issues but I still have the same problem.
> So then I used your .rmd file and it looks like it works ( at least I
don't
> get any error).
>
> Now I have some problems with the assignment as I will get only 1 or 2
> formulas assigned on a list of 144 signals . Any suggestions?
>
> Thank you,
> Angela
>
>
>
> Il giorno gio 9 mar 2023 alle ore 11:21 Simeon Schum <
> ***@***.***> ha scritto:
>
> > Hello Angela,
> >
> > That error suggests that the loading of dplyr is masking some function
in
> > the "stats" package, which is not explicitly used in MFAssignR and
> > shouldn't cause a problem directly. The objects masked from the "base"
> > package may cause an issue if they underpin some of the other functions
> > that I am using in MFAssignR, but I don't call them explicitly in any
of
> > the functions.
> >
> > In this case the biggest issue seems like it has to do with loading R
and
> > the various packages on your computer, I have seen other users have
> issues
> > with getting aspects of this working on Macs before, though I don't
know
> if
> > they had the same issues as you, and it definitely doesn't mean you are
> > doing anything wrong.
> >
> > At the core of the issue I think is just not having the various version
> > agreeing with each other (R and MFAssignR in particular). I had to make
> > some changes to MFAssignR when a newer version of R came out a while
> back.
> > I am attaching the most up to date version of MFAssignR so you can try
to
> > get it installed and see if it works any better for you. It is the same
> > version as is currently on Github, but sometimes it seems like people
> have
> > had issues getting it installed from the Github files.
> >
> > I apologize for the slow response. If you could try to install this new
> > version of MFAssignR (it also may be worth trying to re-install R and
> > RStudio) and let me know what happens that would be good. If you
continue
> > to have problems, please let me know and I will try to respond more
> > promptly.
> >
> > Thanks,
> > Simeon
> >
> > On Thu, Mar 2, 2023 at 11:54 AM AngelaDCP ***@***.***> wrote:
> >
> > > Dear Simeon,
> > > I'm using RStudio Version 2022.12.0+353 on a MacBookPro.
> > >
> > > I'm getting this error and it will cause issues later when I run
> > > MFAssignCHO and MFAssign
> > >
> > > library(dplyr)
> > >
> > > Attaching package: ‘dplyr’
> > >
> > > The following objects are masked from ‘package:stats’:
> > >
> > > filter, lag
> > >
> > >
> > > The following objects are masked from ‘package:base’:
> > >
> > > intersect, setdiff, setequal, union
> > >
> > >
> > > —
> > > Reply to this email directly, view it on GitHub
> > > <
> #27 (comment)
> > >,
> > > or unsubscribe
> > > <
> >
>
https://github.com/notifications/unsubscribe-auth/AF72HFDEEAWEOKYBND6PZG3W2DGC5ANCNFSM6AAAAAAVCCAL7E
> > >
> > > .
> > > You are receiving this because you commented.Message ID:
> > > ***@***.***>
> > >
> >
> > —
> > Reply to this email directly, view it on GitHub
> > <
#27 (comment)
> >,
> > or unsubscribe
> > <
>
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> >
> > .
> > You are receiving this because you authored the thread.Message ID:
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> >
>
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Hi,
thank you so much for this work! It is very helpful!
I'm trying to use MFAssignR for MS data assignment acquired on a FT-ICR. When I run the script I can get the MFAssign for CHO, but then I don't get any assignment when I run MFAssign with Heteroatoms.
I'm wondering if I'm missing something or I wrote something wrong in my script.
Hopefully I can get some help!
Thank you,
best
Angela
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