Hi,
sorry for the wait - I missed this one. Before anything else, in your
script you are using the ACNE pipeline not the CRMAv2. You are saying
"I followed CRMA v2 vignette" - please let me know where you found
that, because if there's a document out there claiming to be CRMAv2
when it's using ACNE, it needs to be fixed.
So, the error originates from NmfSnpPlm, which is part of ACNE not
CRMAv2. I'm happy to help you troubleshoot why NmfSnpPlm complaints,
but then I would need to get the problematic data from you. However,
if you don't mind (allele-specific) CRMAv2 (I use it all the time
myself), then replace everything in the "Probe-processing as in CRMA
v2" section (AllelicCrosstalkCalibration() to getChipEffectSet()) in
your script with:
res <- doASCRMAv2(cs, drop=FALSE, verbose=verbose)
ces <- res$cesN
and then continue as before.
The 'ces' is an CnChipEffectSet object. It should have tags
ACC,-XY,BPN,-XY,AVG,FLN,-XY indicating that (i) allelic crosstalk has
been fitted to all chromosomes by X and Y and applied to all signals
(ACC,-XY), (ii) likewise for base-position normalization (BPN,-XY),
followed by (iii) allele-specific probe summarization using robust
averging (AVG), and finally (iv) fragment-length normalization fitted
to all but X and Y chromosomes and applied to all signals (FLN,-XY).
BTW, the steps done before NmfSnpPlm are the same, so those will be
picked up/won't have to be redone by CRMAv2.
Hope this helps
Henrik
On Tue, Mar 25, 2014 at 11:25 AM, <eric.voi...@gmail.com> wrote:
> Dear Sir or Madam,
>
> I would like to analyse Affymetrix Mouse Diversity Array, extract BAF LRR
> using CRMA v2
> I followed CRMA v2 vignette, and I get always an error during process() :
>
> ---
> 20140319 18:52:29| Reading probe intensities from 17 arrays...done
> 20140319 18:52:29| Fitting probe-level model...
> 20140319 18:52:29| Calling fitUnit() via lapply()
> Erreur dans if (sampleAA * sampleBB > 0L) { :
> l'argument est de longueur nulle
> Calls: fit ... fit.ProbeLevelModel -> <Anonymous> -> FUN -> nmfFcn ->
> robustWInit
> De plus : Il y a eu 45 avis (utilisez warnings() pour les visionner)
> 20140319 18:55:34| Fitting probe-level model...done
> 20140319 18:55:34| Fitting chunk #1 of 6 of 'genotyping' units (code=2)
> with 4 groups/2+2+2+2 cells...done
> 20140319 18:55:34| Unit dimension #1 (4 groups/2+2+2+2 cells) of 4...done
> 20140319 18:55:34| Fitting the model by unit dimensions (at least for the
> large classes)...done
> 20140319 18:55:34| Unit type #2 ('genotyping') of 2...done
> 20140319 18:55:34| Fitting NmfSnpPlm for each unit type separately...done
> 20140319 18:55:34|Fitting model of class NmfSnpPlm...done
> Exécution arrêtée
> ----
>
> All packages are updated with the latest releases.
>
> here is sessionInfo()
> http://eric.voirin.free.fr/aroma/sessionInfo.Rout
>
> here is the script
> http://eric.voirin.free.fr/aroma/script_aroma.R
>
> here is the logfile
> http://eric.voirin.free.fr/aroma/script_aroma.Rout
>
> Easy to reprodruce.
> Thanks in advance for your time and ideas...
>
> Eric
>
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