[BioC] A question about lowess normalization

[Gustavo Henrique Esteves]

There is another way to overcome this type of problem,  that uses a
smooth background correction to spots that have intensity <
background. This method was proposed by David Edwards in 2003 and was
published in Bioinformatics, v 19, pp 825-833.

Best regards,

Gustavo




On Sun, 5 Dec 2004 20:56:15 -0600, Tony Kowal <askowal at northwestern.edu> wrote:
> Hi All,
> 
> I have just started using R / Bioconductor within the last couple of
> weeks to analyze our microarray data.  While attempting to do the Print
> Tip Lowess normalization on a particular scan, I received the following
> error, and was unable to proceed with the analysis.  I did a google
> search for the error message, but I am still unclear about what is
> wrong with my data.  I have provided the warning I recieved, as well as
> the list of warning that I requested.  If anyone can provide some
> suggestions, I will be extremely grateful.
> 
> There are a fairly large number of NA's in my data.  I am using R 2.0
> with the most recent version of Bioconductor.  Analysis is being done
> on a Gateway PC.
> 
> Thanks in advance,
> Tony
> 
> > Error in simpleLoess(y, x, w, span, degree, parametric, drop.square,
> > normalize,  :
> >         NA/NaN/Inf in foreign function call (arg 1)
> > In addition: There were 50 or more warnings (use warnings() to see the
> > first 50)
> >>  warnings()
> > Warning messages:
> > 1: zero-width neighborhood. make span bigger
> > 2: ihat=1 (diag L) in l2fit only makes sense if z=x (eval=data).
> > 3: zero-width neighborhood. make span bigger
> > 4: zero-width neighborhood. make span bigger
> > 5: ihat=1 (diag L) in l2fit only makes sense if z=x (eval=data).
> > 6: zero-width neighborhood. make span bigger
> > 7: zero-width neighborhood. make span bigger
> > 8: ihat=1 (diag L) in l2fit only makes sense if z=x (eval=data).
> > 9: zero-width neighborhood. make span bigger
> > 10: zero-width neighborhood. make span bigger
> > 11: ihat=1 (diag L) in l2fit only makes sense if z=x (eval=data).
> > 12: zero-width neighborhood. make span bigger
> > 13: zero-width neighborhood. make span bigger
> > 14: ihat=1 (diag L) in l2fit only makes sense if z=x (eval=data).
> > 15: zero-width neighborhood. make span bigger
> > 16: zero-width neighborhood. make span bigger
> > 17: ihat=1 (diag L) in l2fit only makes sense if z=x (eval=data).
> > 18: zero-width neighborhood. make span bigger
> > 19: zero-width neighborhood. make span bigger
> > 20: ihat=1 (diag L) in l2fit only makes sense if z=x (eval=data).
> > 21: zero-width neighborhood. make span bigger
> > 22: zero-width neighborhood. make span bigger
> > 23: ihat=1 (diag L) in l2fit only makes sense if z=x (eval=data).
> > 24: zero-width neighborhood. make span bigger
> > 25: zero-width neighborhood. make span bigger
> > 26: ihat=1 (diag L) in l2fit only makes sense if z=x (eval=data).
> > 27: zero-width neighborhood. make span bigger
> > 28: zero-width neighborhood. make span bigger
> > 29: ihat=1 (diag L) in l2fit only makes sense if z=x (eval=data).
> > 30: zero-width neighborhood. make span bigger
> > 31: zero-width neighborhood. make span bigger
> > 32: ihat=1 (diag L) in l2fit only makes sense if z=x (eval=data).
> > 33: zero-width neighborhood. make span bigger
> > 34: ihat=1 (diag L) in l2fit only makes sense if z=x (eval=data).
> > 35: zero-width neighborhood. make span bigger
> > 36: ihat=1 (diag L) in l2fit only makes sense if z=x (eval=data).
> > 37: zero-width neighborhood. make span bigger
> > 38: zero-width neighborhood. make span bigger
> > 39: ihat=1 (diag L) in l2fit only makes sense if z=x (eval=data).
> > 40: zero-width neighborhood. make span bigger
> > 41: zero-width neighborhood. make span bigger
> > 42: ihat=1 (diag L) in l2fit only makes sense if z=x (eval=data).
> > 43: zero-width neighborhood. make span bigger
> > 44: zero-width neighborhood. make span bigger
> > 45: ihat=1 (diag L) in l2fit only makes sense if z=x (eval=data).
> > 46: zero-width neighborhood. make span bigger
> > 47: zero-width neighborhood. make span bigger
> > 48: ihat=1 (diag L) in l2fit only makes sense if z=x (eval=data).
> > 49: zero-width neighborhood. make span bigger
> > 50: zero-width neighborhood. make span bigger
> 
> Tony Kowal
> Graduate Student
>         Department of Cell and Molecular Biology
> Northwestern University
> Chisholm Lab
> 303 E. Chicago Ave.
> Rm 11-100
> Chicago, IL 60611
> 
> e-mail: askowal at northwestern.edu
> 
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> https://stat.ethz.ch/mailman/listinfo/bioconductor
> 


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Gustavo Henrique Esteves

e-mail: gesteves at gmail.com
Home Page: http://www.vision.ime.usp.br/~gesteves/