[BioC] warning messages in gcrma

[James MacDonald]

These warnings are due to some changes that are occuring in R. They
don't have any effect on your results, and they will go away with the
new release of BioC.

Best,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
>>> <paolo.sirabella at uniroma1.it> 03/16/04 8:28 AM >>>
I got the same kind of warnings referred in the attached post by Lizhe
Xu. The 
configuration is R1.8.1/BioC1.3/Linux .
I have no idea of the meaning of these warnings and if they are
significant.

Does anyone give us some hints ?

Thanks

----------------------------------------------------------------
Paolo Sirabella, PhD
University of Rome - "La Sapienza"
Dept. of Human Physiology and Pharmacology - Building of Human
Physiology
P.le Aldo Moro, 5 - 00185 Roma - Italy
Web http://w3.uniroma1.it/cisb/Cisb/members/sirabella

Simplex Sigillum Veri
------------------------------------------------------------------------


On 15 Mar 2004 at 15:22, Lizhe Xu wrote:

> I just tried to run gcrma and got 30 warnings. I wonder if there are
something I did wrong and if these warning affect my results. Thanks.
> 
> > gcrmaDataB<-gcrma(DataB)
> Loading required package: hgu133bprobe 
> Loading required package: matchprobes 
> background correction: gcrma 
> normalization: quantiles 
> PM/MM correction : pmonly 
> expression values: medianpolish 
> background correcting...There were 30 warnings (use warnings() to see
them)
> done.
> normalizing...done.
> 22645 ids to be processed
> .........
> > warnings()
> Warning messages:
> 1: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 2: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 3: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 4: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 5: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 6: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 7: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 8: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 9: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 10: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 11: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 12: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 13: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 14: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 15: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 16: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 17: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 18: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 19: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 20: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 21: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 22: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 23: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 24: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 25: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 26: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 27: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 28: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 29: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 30: multi-argument returns are deprecated in: return(y = yhat, wt) 
> 
> Lizhe

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