[BioC] A question about lowess normalization

[Tony Kowal]

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