Hi,
I am trying to analyze some quantarray files using limma Guide, when
suddenly it gives me the following error at the background
normalization
step (using normexp method and offset = 50)
Error in if (all(abs(delta) < 1e-10)) break :
missing value where TRUE/FALSE needed
I can't find why this happens.
Does anyone an idea of what is happening?
--
regards
Henrique Proen?a
Hi Henrique,
I recently got the same error with a Nimblegen dataset. Because in
this
dataset the background is actually not provided (the corresponding
column is
all-zero), I figured that was the reason ... However, this error
occurs only
with R-2.7.0, not with 2.6 or 2.5. So something must have changed in
the
optim() function (this is where it crashes in my case).
Glad to hear that I am not the only one who stumbled across this !
Ulrike
On Thursday 10 July 2008 17:13, Henrique Proen?a wrote:
> Hi,
>
> I am trying to analyze some quantarray files using limma Guide, when
> suddenly it gives me the following error at the background
normalization
> step (using normexp method and offset = 50)
>
> Error in if (all(abs(delta) < 1e-10)) break :
> missing value where TRUE/FALSE needed
>
> I can't find why this happens.
> Does anyone an idea of what is happening?
--
Dr. Ulrike Goebel
Bioinformatics Support
Max-Planck Institute for Plant Breeding Research
Carl-von-Linne Weg 10
50829 Cologne
Germany
+49(0) 221 5062 121
Dear Ulrike and Henrique,
The problem is more likely to be with the limma normexp.fit() function
than with optim().
There is a rare numerical instability which causes an error like this
with
normexp background correction in limma 2.14.X. Jeremy Silver and I
did a
lot of work on this late last year, and we think we have eliminated
the
problem. The new (faster) code is in limma on the Bioconductor
developmental repository. You can try it out if you install R 2.8.0.
I'd
be interested to know if it solves the problem for your data sets.
Best wishes
Gordon
> Date: Thu, 10 Jul 2008 17:35:51 +0200
> From: Ulrike Goebel <ugoebel at="" mpiz-koeln.mpg.de="">
> Subject: Re: [BioC] limma background correction
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <200807101735.52255.ugoebel at mpiz-koeln.mpg.de>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Henrique,
>
> I recently got the same error with a Nimblegen dataset. Because in
this
> dataset the background is actually not provided (the corresponding
column is
> all-zero), I figured that was the reason ... However, this error
occurs only
> with R-2.7.0, not with 2.6 or 2.5. So something must have changed in
the
> optim() function (this is where it crashes in my case).
>
> Glad to hear that I am not the only one who stumbled across this !
>
> Ulrike
>
> On Thursday 10 July 2008 17:13, Henrique Proen?a wrote:
>> Hi,
>>
>> I am trying to analyze some quantarray files using limma Guide,
when
>> suddenly it gives me the following error at the background
normalization
>> step (using normexp method and offset = 50)
>>
>> Error in if (all(abs(delta) < 1e-10)) break :
>> missing value where TRUE/FALSE needed
>>
>> I can't find why this happens.
>> Does anyone an idea of what is happening?
>
> --
> Dr. Ulrike Goebel
> Bioinformatics Support
> Max-Planck Institute for Plant Breeding Research
> Carl-von-Linne Weg 10
> 50829 Cologne
> Germany
> +49(0) 221 5062 121
Dear Gordon,
I have tried the 2.15.10 version of limma with R 2.8.0 and it works
fine
for the data set that previously gave errors.
Thanks a lot for your help.
Regards
Henrique Proen?a
--------------------------
Gordon K Smyth wrote:
> Dear Ulrike and Henrique,
>
> The problem is more likely to be with the limma normexp.fit()
function
> than with optim().
>
> There is a rare numerical instability which causes an error like
this
> with normexp background correction in limma 2.14.X. Jeremy Silver
and I
> did a lot of work on this late last year, and we think we have
> eliminated the problem. The new (faster) code is in limma on the
> Bioconductor developmental repository. You can try it out if you
> install R 2.8.0. I'd be interested to know if it solves the problem
for
> your data sets.
>
> Best wishes
> Gordon
>
>> Date: Thu, 10 Jul 2008 17:35:51 +0200
>> From: Ulrike Goebel <ugoebel at="" mpiz-koeln.mpg.de="">
>> Subject: Re: [BioC] limma background correction
>> To: bioconductor at stat.math.ethz.ch
>> Message-ID: <200807101735.52255.ugoebel at mpiz-koeln.mpg.de>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi Henrique,
>>
>> I recently got the same error with a Nimblegen dataset. Because in
this
>> dataset the background is actually not provided (the corresponding
>> column is
>> all-zero), I figured that was the reason ... However, this error
>> occurs only
>> with R-2.7.0, not with 2.6 or 2.5. So something must have changed
in the
>> optim() function (this is where it crashes in my case).
>>
>> Glad to hear that I am not the only one who stumbled across this !
>>
>> Ulrike
>>
>> On Thursday 10 July 2008 17:13, Henrique Proen?a wrote:
>>> Hi,
>>>
>>> I am trying to analyze some quantarray files using limma Guide,
when
>>> suddenly it gives me the following error at the background
normalization
>>> step (using normexp method and offset = 50)
>>>
>>> Error in if (all(abs(delta) < 1e-10)) break :
>>> missing value where TRUE/FALSE needed
>>>
>>> I can't find why this happens.
>>> Does anyone an idea of what is happening?
>>
>> --
>> Dr. Ulrike Goebel
>> Bioinformatics Support
>> Max-Planck Institute for Plant Breeding Research
>> Carl-von-Linne Weg 10
>> 50829 Cologne
>> Germany
>> +49(0) 221 5062 121
>
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