Hello dear List,
I conducted an analysis with EdgeR and I thank you for this software.
I have a list of DE genes after treatment A and one after treatment B.
using the cntrast fucntion, I also have the comparison of A and B,
which shows 43 differentially regulated genes. When I check FDR and
logFC fot those 43 genes, they are signicant.
But when I come back to list A or B,
I see that some of those 43 genes did not reach significance either
for FDR or for logFC, in either list A or B.
Should I then get rid of those genes,
or FDR in the contrast output takes that into account ?
thanks a lot for you answers,
best regards,
anna
-- output of sessionInfo():
R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
[5] LC_TIME=French_France.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
--
Sent via the guest posting facility at bioconductor.org.
hi again everybody,
actually log FC is not a worry because I can choose a cut-off myself (
logFC>1 for example),
the worry is more about FDR that are >0.05 in list A or B, but still
the gene has FDR<0.05 in the contrast list,
so is that gene significantly differently regulated ?
thanks,
anna
-- output of sessionInfo():
R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
[5] LC_TIME=French_France.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
--
Sent via the guest posting facility at bioconductor.org.
Hi Anna,
On 11/3/2012 10:23 AM, anna [guest] wrote:
> hi again everybody,
> actually log FC is not a worry because I can choose a cut-off myself
( logFC>1 for example),
> the worry is more about FDR that are>0.05 in list A or B, but still
the gene has FDR<0.05 in the contrast list,
> so is that gene significantly differently regulated ?
If I understand what you have done, you are asking three different
questions:
Is a gene differentially expressed after treatment A
Is a gene differentially expressed after treatment B
Is a gene differentially expressed when comparing treatment A to
treatment B
So if I assume that questions 1 & 2 are treatment/control, and
question
3 is treatment A/treatment B, then there are several scenarios where 1
&
2 wouldn't be significant, but 3 would. For instance:
Gene x goes down in treatment A vs control, but not significantly.
Gene x goes up in treatment B vs control, but not significantly.
Gene x is significantly different between treatment A and treatment B,
because the gene goes in different directions in each treatment, and
when comparing the treatments this difference is large enough to be
significant.
Best,
Jim
> thanks,
> anna
>
> -- output of sessionInfo():
>
> R version 2.15.1 (2012-06-22)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
> [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
> [5] LC_TIME=French_France.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
Anna,
I found your question difficult to interpret.
If I understand your question correctly, you have compared a treatment
A
back to a control treatment, and you have also compared treatment B
back
to the control. So you have contrasts AvsControl and BvsControl.
Now you make the contrast BvsControl-AvsControl, and you find some
genes
significant that were not significant for either BvsControl or
AvsControl.
This is not a mistake, and it's no great mystery. It can easily be
that B
is higher than the Control for some gene, but not by enough to reach
signficance, and A is less the control for the same gene, but not by
enough to reach significance, but the combined difference B vs A is
large
enough to be significantly greater than zero. This is just because
B-A is
larger than either B-Control or A-Control. In such cases, you know
that A
and B are different, but it is not necessarily discernible whether
both or
just one are different from the control.
How you interpret such genes depends on your scientific questions. We
can't tell you how to do that.
Best wishes
Gordon
PS. Please check over the posting guide, which has been expanded
recently:
http://www.bioconductor.org/help/mailing-list/posting-guide/
--------- original message --------
[BioC] EdgeR: about FDR
anna [guest] guest at bioconductor.org
Sat Nov 3 14:22:38 CET 2012
Hello dear List,
I conducted an analysis with EdgeR and I thank you for this software.
I have a list of DE genes after treatment A and one after treatment B.
using the cntrast fucntion, I also have the comparison of A and B,
which
shows 43 differentially regulated genes. When I check FDR and logFC
fot
those 43 genes, they are signicant.
But when I come back to list A or B,
I see that some of those 43 genes did not reach significance either
for
FDR or for logFC, in either list A or B.
Should I then get rid of those genes,
or FDR in the contrast output takes that into account ?
thanks a lot for you answers,
best regards,
anna
-- output of sessionInfo():
R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
[5] LC_TIME=French_France.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
______________________________________________________________________
The information in this email is confidential and
intend...{{dropped:4}}
Hello James, (Hello Gordon)
thank you very much for your help,(both of you).
I understand pretty well what you mean James,thank you.
I was just wondering how we can build certainty on 2 uncertainties.
But I check back my data , actually there was not absence of
significance at the same time for both treatments,
it only happened that one of them at a time was not significantly
regulating some genes(either same or opposite direction as the other
treatment). So then if I assume that for those genes in that treatment
logFc=0,
I still had a large enough difference between treatment A and B, which
reaches significance.
Have a nice day James,
thanks again,
anna
-- output of sessionInfo():
R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
[5] LC_TIME=French_France.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
--
Sent via the guest posting facility at bioconductor.org.