Dear Bioconductor,
I have a problem running vst in lumi, where I'm getting the following
error:
"
> mydata.lumi.B = lumiB(mydata.lumi, method='forcePositive')
> mydata.lumi.B.T = lumiT(mydata.lumi.B)
2007-07-10 12:29:57 , processing array 1
2007-07-10 12:29:58 , processing array 2
2007-07-10 12:29:59 , processing array 3
2007-07-10 12:29:59 , processing array 4
2007-07-10 12:29:59 , processing array 5
Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...)
:
0 (non-NA) cases
"
When I change the transformation method in lumiT to 'log2', or to
'cubicRoot', I don't get any error message. I have got this
behaviour on both Mac OS X and Windows XP platforms.
Thanks,
Will
--
William Mifsud
Wellcome Trust/Cancer Research UK Gurdon Institute
Tennis Court Road
Cambridge
CB2 1QN
Hi Will,
Can you provide the sessionInfo()? Like the version of lumi you are
using. I
guess you are using the old version of lumi. Thanks!
Pan
On 7/12/07 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at="" stat.math.ethz.ch=""> wrote:
> Message: 1
> Date: Wed, 11 Jul 2007 11:25:53 +0100
> From: William Mifsud <wm237 at="" cam.ac.uk="">
> Subject: [BioC] lumiT VST error
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <c04f805e-e42d-4091-bdd2-f707b4b1ebf4 at="" cam.ac.uk="">
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
> Dear Bioconductor,
>
> I have a problem running vst in lumi, where I'm getting the
following
> error:
>
> "
>> mydata.lumi.B = lumiB(mydata.lumi, method='forcePositive')
>> mydata.lumi.B.T = lumiT(mydata.lumi.B)
> 2007-07-10 12:29:57 , processing array 1
> 2007-07-10 12:29:58 , processing array 2
> 2007-07-10 12:29:59 , processing array 3
> 2007-07-10 12:29:59 , processing array 4
> 2007-07-10 12:29:59 , processing array 5
> Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok,
...) :
> 0 (non-NA) cases
> "
>
> When I change the transformation method in lumiT to 'log2', or to
> 'cubicRoot', I don't get any error message. I have got this
> behaviour on both Mac OS X and Windows XP platforms.
>
> Thanks,
>
> Will
> --
>
> William Mifsud
> Wellcome Trust/Cancer Research UK Gurdon Institute
> Tennis Court Road
> Cambridge
> CB2 1QN
>
> Can you provide the sessionInfo()? Like the version of lumi you are
> using. I
> guess you are using the old version of lumi. Thanks!
It's lumi 1.2.0 - I had also got the same error with several previous
versions of lumi.
> sessionInfo()
R version 2.5.0 (2007-04-23)
i386-pc-mingw32
locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
Kingdom.1252;LC_MONETARY=English_United Kingdom.
1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
attached base packages:
[1] "grid" "tools" "stats" "graphics" "grDevices"
"utils" "datasets" "methods" "base"
other attached packages:
lumiMouseV1 lumi mgcv biomaRt
RCurl XML beadarray beadarraySNP quantsmooth lodplot
"1.2.0" "1.2.0" "1.3-25" "1.10.0"
"0.8-0" "1.9-0" "1.4.0" "1.2.0" "1.2.0"
"1.1"
quantreg SparseM affy affyio
geneplotter lattice annotate Biobase limma
"4.06" "0.72" "1.14.1" "1.4.0" "1.14.0"
"0.15-4" "1.14.1" "1.14.0" "2.10.5"
Thanks,
Will
--
The latest version is 1.3.16, which should be downloaded from
Bioconductor
developing section:
http://www.bioconductor.org/packages/2.1/bioc/html/lumi.html
Tell me if error still exists when using the new version.
Pan
On 7/12/07 9:25 AM, "William Mifsud" <wm237 at="" cam.ac.uk=""> wrote:
>>
>> Can you provide the sessionInfo()? Like the version of lumi you are
>> using. I
>> guess you are using the old version of lumi. Thanks!
>
> It's lumi 1.2.0 - I had also got the same error with several
previous
> versions of lumi.
>
>> sessionInfo()
> R version 2.5.0 (2007-04-23)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_MONETARY=English_United Kingdom.
> 1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] "grid" "tools" "stats" "graphics" "grDevices"
> "utils" "datasets" "methods" "base"
>
> other attached packages:
> lumiMouseV1 lumi mgcv biomaRt
> RCurl XML beadarray beadarraySNP quantsmooth
lodplot
> "1.2.0" "1.2.0" "1.3-25" "1.10.0"
> "0.8-0" "1.9-0" "1.4.0" "1.2.0" "1.2.0"
"1.1"
> quantreg SparseM affy affyio
> geneplotter lattice annotate Biobase limma
> "4.06" "0.72" "1.14.1" "1.4.0" "1.14.0"
> "0.15-4" "1.14.1" "1.14.0" "2.10.5"
>
>
> Thanks,
>
> Will
---------------------------------------------------
Pan Du, PhD
Research Associate / Senior Bioinformatics Analyst
Robert H. Lurie Comprehensive Cancer Center
Northwestern University
676 ST Clair St., #1200
Chicago, IL 60611
Office (312)695-4781
dupan at northwestern.edu
Dear list,
I'm looking for the source codes for affy,gcrma and quantiles.
Can anyone tell me where to find themn ?
Gunther
-----Urspr?ngliche Nachricht-----
Von: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] Im Auftrag von Pan
Du
Gesendet: Donnerstag, 12. Juli 2007 16:39
An: William Mifsud; bioconductor at stat.math.ethz.ch
Betreff: Re: [BioC] lumiT VST error
The latest version is 1.3.16, which should be downloaded from
Bioconductor
developing section:
http://www.bioconductor.org/packages/2.1/bioc/html/lumi.html
Tell me if error still exists when using the new version.
Pan
On 7/12/07 9:25 AM, "William Mifsud" <wm237 at="" cam.ac.uk=""> wrote:
>>
>> Can you provide the sessionInfo()? Like the version of lumi you are
>> using. I guess you are using the old version of lumi. Thanks!
>
> It's lumi 1.2.0 - I had also got the same error with several
previous
> versions of lumi.
>
>> sessionInfo()
> R version 2.5.0 (2007-04-23)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_MONETARY=English_United Kingdom.
> 1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] "grid" "tools" "stats" "graphics" "grDevices"
> "utils" "datasets" "methods" "base"
>
> other attached packages:
> lumiMouseV1 lumi mgcv biomaRt
> RCurl XML beadarray beadarraySNP quantsmooth
lodplot
> "1.2.0" "1.2.0" "1.3-25" "1.10.0"
> "0.8-0" "1.9-0" "1.4.0" "1.2.0" "1.2.0"
"1.1"
> quantreg SparseM affy affyio
> geneplotter lattice annotate Biobase limma
> "4.06" "0.72" "1.14.1" "1.4.0" "1.14.0"
> "0.15-4" "1.14.1" "1.14.0" "2.10.5"
>
>
> Thanks,
>
> Will
---------------------------------------------------
Pan Du, PhD
Research Associate / Senior Bioinformatics Analyst Robert H. Lurie
Comprehensive Cancer Center Northwestern University
676 ST Clair St., #1200
Chicago, IL 60611
Office (312)695-4781
dupan at northwestern.edu
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Hallo Gunther,
> Dear list,
>
> I'm looking for the source codes for affy,gcrma and quantiles.
>
> Can anyone tell me where to find themn ?
>
> Gunther
There are many ways. One is:
Go to http://www.bioconductor.org
Click on "For Developers"
Click on "svn repository"
Another one is to unpack the package "source" tar-balls.
Best wishes
Wolfgang
------------------------------------------------------------------
Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
Dear Pan,
> The latest version is 1.3.16, which should be downloaded from
> Bioconductor
> developing section:
> http://www.bioconductor.org/packages/2.1/bioc/html/lumi.html
>
> Tell me if error still exists when using the new version.
Thanks for this - I got no error with 1.3.16.
Will
--
