[BioC] Limma - error when using duplicateCorrelation

[Gordon K Smyth]

Dear Jacob,

Try identifying which gene is causing the error.  Edit the function duplicateCorrelation, by using
fix(duplicateCorrelation), to add the line

   cat(i,"\n")

immediately before the line

   y <- drop(M[i, ])

Then try running duplicateCorrelation() again.  This will tell you which gene is causing the problem.

Suppose the problem is at gene 10000.  Looking at the data

  MA[10000,]

may tell you what the problem is.  Alternatively it might be enough to simply remove the offending
gene from the duplicateCorrelation calculation by

  duplicateCorrelation(MA[-10000,],design)

Removing one gene will not make any material different to the computed value.

Best wishes
Gordon

> -----Oprindelig meddelelse-----
> Fra: Gordon K Smyth [mailto:smyth at wehi.EDU.AU]
> Sendt: Tuesday, October 10, 2006 1:21 PM
> Til: Jakob Hedegaard
> Cc: bioconductor at stat.math.ethz.ch
> Emne: [BioC] Limma - error when using duplicateCorrelation
>
> Dear Jakob,
>
> I've never seen this error, despite using duplicateCorrelation() often.  Please provide a
> reproducible example so that the error can be tracked down.
>
> Best wishes
> Gordon
>
>> Date: Tue, 10 Oct 2006 09:06:20 +0200
>> From: "Jakob Hedegaard" <Jakob.Hedegaard at agrsci.dk>
>> Subject: [BioC] Limma - error when using duplicateCorrelation
>> To: <bioconductor at stat.math.ethz.ch>
>>
>> Hi List
>>
>> When using duplicateCorrelation in Limma I am receiving the following error:
>>
>>> cor <- duplicateCorrelation(MA, design=design, ndups=2,
>>> weights=MA$weights)
>> Error in La.svd(QtZ, nu = mq, nv = 0) : error code 1 from Lapack routine 'dgesdd'
>>
>> - any suggestions would be appreciated....
>>
>>> sessionInfo()
>> Version 2.3.1 (2006-06-01)
>> x86_64-unknown-linux-gnu
>>
>> attached base packages:
>> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
>> [7] "base"
>>
>> other attached packages:
>>  statmod    limma
>>  "1.2.4" "2.7.10"
>>
>>
>>
>> Best regards
>>
>> Jakob Hedegaard
>> Project scientist
>>
>>
>>
>>  	 Danish Institute of Agricultural Sciences Research Centre Foulum
>> Dept. of Genetics and Biotechnology Blichers Allé 20, P.O. BOX 50
>> DK-8830 Tjele
>>
>> Phone:	 +45 8999 1900
>> Direct:	 +45 8999 1363
>> E-mail:	 Jakob.Hedegaard at agrsci.dk <mailto:Jakob.Hedegaard at agrsci.dk>
>> Web:	 www.agrsci.org <http://www.agrsci.org/>