I am wondering as a biologist what a negative B value might mean in
the top
genes table and on a volcano plot. Does it mean something is
confidently not
moving (as B is related to movement) or is it just crap data?
Thanks for your opinions in advance,
Liz
Molteno Building
Department of Pathology
University of Cambridge
Tennis Court Road
Cambridge, CB2 1QP
United Kingdom
Website: http://www.path.cam.ac.uk/~toxo/
Tel 01223 33 33 31(office) or 01223 33 33 29 (lab)
[[alternative HTML version deleted]]
Liz,
It isn't a measure of data quality. It is a measure of the likelihood
of differential expression. Negative values mean odds are that it is
not differentially expressed.
Sean
On Aug 19, 2004, at 7:53 AM, Elizabeth Brooke-Powell wrote:
> I am wondering as a biologist what a negative B value might mean in
> the top
> genes table and on a volcano plot. Does it mean something is
> confidently not
> moving (as B is related to movement) or is it just crap data?
>
> Thanks for your opinions in advance,
>
> Liz
>
> Molteno Building
> Department of Pathology
> University of Cambridge
> Tennis Court Road
> Cambridge, CB2 1QP
> United Kingdom
>
> Website: http://www.path.cam.ac.uk/~toxo/
> Tel 01223 33 33 31(office) or 01223 33 33 29 (lab)
>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
Sean,
Thanks for getting back to me so quickly, just so I follow your
explanation,
the more negative the number i.e. -6 vs -1 the greater the odds of it
not
being expressed? What does having a negative number actually mean in
relationship to 0 or a positive number?
Thanks again,
Liz
-----Original Message-----
From: Sean Davis [mailto:sdavis2@mail.nih.gov]
Sent: 19 August 2004 13:33
To: Elizabeth Brooke-Powell
Cc: Bioconductor
Subject: Re: [BioC] B statistic in limmaGUI
Liz,
It isn't a measure of data quality. It is a measure of the likelihood
of differential expression. Negative values mean odds are that it is
not differentially expressed.
Sean
Liz,
B is a lod (logarithm of the odds), so even odds (1:1) are given a
value of 0. Better than average is positive and worse is negative.
Sean
On Aug 19, 2004, at 8:43 AM, Elizabeth Brooke-Powell wrote:
> Sean,
>
> Thanks for getting back to me so quickly, just so I follow your
> explanation,
> the more negative the number i.e. -6 vs -1 the greater the odds of
it
> not
> being expressed? What does having a negative number actually mean in
> relationship to 0 or a positive number?
>
> Thanks again,
>
> Liz
>
> -----Original Message-----
> From: Sean Davis [mailto:sdavis2@mail.nih.gov]
> Sent: 19 August 2004 13:33
> To: Elizabeth Brooke-Powell
> Cc: Bioconductor
> Subject: Re: [BioC] B statistic in limmaGUI
>
> Liz,
>
> It isn't a measure of data quality. It is a measure of the
likelihood
> of differential expression. Negative values mean odds are that it
is
> not differentially expressed.
>
> Sean
>
>
Hi Sean,
Does +ve mean better then average odds that it is differentially
expressed
and therefore does the more -ve mean that the odds are greater that it
is
not differentially expressed? Is there some meaning that the lowest B
values
tend to be about -6?
Liz
-----Original Message-----
From: Sean Davis [mailto:sdavis2@mail.nih.gov]
Sent: 19 August 2004 13:59
To: Elizabeth Brooke-Powell
Cc: bioconductor@stat.math.ethz.ch
Subject: Re: [BioC] B statistic in limmaGUI
Liz,
B is a lod (logarithm of the odds), so even odds (1:1) are given a
value of 0. Better than average is positive and worse is negative.
Sean
Hi Sean,
Thanks for your help, and here is our final question on this matter.
We are
interested in things that do not move. From our current understanding
(maybe
completely wrong) that analogous to finding things that move (are
differentially expressed) should we ask for B values from some
negative
value to the lowest B value?
Thanks again,
Liz
-----Original Message-----
From: Sean Davis [mailto:sdavis2@mail.nih.gov]
Sent: 19 August 2004 15:28
To: Elizabeth Brooke-Powell
Subject: Re: [BioC] B statistic in limmaGUI
I have yet to hear from anyone else regarding the "realistic"
interpretation of the B-values, but negative B-values are not very
interesting (they are more than likely not differentially expressed).
Also, I don't know if there is any deep meaning in the minimum B
value.
Sean
On Aug 19, 2004, at 9:09 AM, Elizabeth Brooke-Powell wrote:
> Hi Sean,
>
> Does +ve mean better then average odds that it is differentially
> expressed
> and therefore does the more -ve mean that the odds are greater that
it
> is
> not differentially expressed? Is there some meaning that the lowest
B
> values
> tend to be about -6?
>
> Liz
>
>
On Thu, 19 Aug 2004, Elizabeth Brooke-Powell wrote:
> We are
> interested in things that do not move. From our current
> understanding
Hi Liz,
The tests for differential expression in limma, limmaGUI etc.
are generally set up to test for differential expression, rather
than lack of it. If you ask the question "How many genes are
not differentially expressed in one comparison?", the answer
would usually be thousands of genes! By looking at the most
negative B statistics, you are not only looking at genes whose
expression levels are unchanged, but you could also be looking
at genes whose changes in expression are extremely variable
between replicate arrays (so they are not ranked as high as
genes whose changes in expression are perfectly consistent
between replicates).
It is natural to get noise around M=0, i.e. there are
usually lots of genes which are not differentially expressed,
but do not all sit exactly on M=0.
If you want to narrow down the list a bit, you could try using
limma from the command-line (using the function classifyTestsF),
to ask questions like "Which genes are differentially expressed
in one comparison, but are not differentially expressed in
another comparison?".
Hope this helps,
James
James,
Thank you for that extra information, very well explained, and makes a
lot
of sense.
Liz
-----Original Message-----
From: James Wettenhall [mailto:wettenhall@wehi.edu.au]
Sent: 20 August 2004 08:05
To: Elizabeth Brooke-Powell
Cc: 'Sean Davis'; bioconductor@stat.math.ethz.ch
Subject: RE: [BioC] B statistic in limmaGUI
On Thu, 19 Aug 2004, Elizabeth Brooke-Powell wrote:
> We are
> interested in things that do not move. From our current
> understanding
Hi Liz,
The tests for differential expression in limma, limmaGUI etc.
are generally set up to test for differential expression, rather
than lack of it. If you ask the question "How many genes are
not differentially expressed in one comparison?", the answer
would usually be thousands of genes! By looking at the most
negative B statistics, you are not only looking at genes whose
expression levels are unchanged, but you could also be looking
at genes whose changes in expression are extremely variable
between replicate arrays (so they are not ranked as high as
genes whose changes in expression are perfectly consistent
between replicates).
It is natural to get noise around M=0, i.e. there are
usually lots of genes which are not differentially expressed,
but do not all sit exactly on M=0.
If you want to narrow down the list a bit, you could try using
limma from the command-line (using the function classifyTestsF),
to ask questions like "Which genes are differentially expressed
in one comparison, but are not differentially expressed in
another comparison?".
Hope this helps,
James
What is the difference between a B value of 1 vs 2 vs 10? How high
can a B value go?
Thanks,
Jason
________________________________
From: bioconductor-bounces@stat.math.ethz.ch on behalf of Elizabeth
Brooke-Powell
Sent: Thu 8/19/2004 11:48 AM
To: 'Sean Davis'
Cc: bioconductor@stat.math.ethz.ch
Subject: RE: [BioC] B statistic in limmaGUI
Hi Sean,
Thanks for your help, and here is our final question on this matter.
We are
interested in things that do not move. From our current understanding
(maybe
completely wrong) that analogous to finding things that move (are
differentially expressed) should we ask for B values from some
negative
value to the lowest B value?
Thanks again,
Liz
-----Original Message-----
From: Sean Davis [mailto:sdavis2@mail.nih.gov]
Sent: 19 August 2004 15:28
To: Elizabeth Brooke-Powell
Subject: Re: [BioC] B statistic in limmaGUI
I have yet to hear from anyone else regarding the "realistic"
interpretation of the B-values, but negative B-values are not very
interesting (they are more than likely not differentially expressed).
Also, I don't know if there is any deep meaning in the minimum B
value.
Sean
On Aug 19, 2004, at 9:09 AM, Elizabeth Brooke-Powell wrote:
> Hi Sean,
>
> Does +ve mean better then average odds that it is differentially
> expressed
> and therefore does the more -ve mean that the odds are greater that
it
> is
> not differentially expressed? Is there some meaning that the lowest
B
> values
> tend to be about -6?
>
> Liz
>
>
_______________________________________________
Bioconductor mailing list
Bioconductor@stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/bioconductor
