[BioC] A question about lowess normalization
Gustavo Henrique Esteves
gesteves at gmail.com
Mon Dec 6 10:52:44 CET 2004
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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
--
_______________________________________________________________
"The truth you speak has no past and no future. It is, and
that's all it needs to be."
"A verdade que você fala não tem passado nem futuro. Ela é,
e isso é tudo que ela precisa ser."
Autor desconhecido
_______________________________________________________________
Gustavo Henrique Esteves
e-mail: gesteves at gmail.com
Home Page: http://www.vision.ime.usp.br/~gesteves/
More information about the Bioconductor
mailing list