[BioC] A question about lowess normalization
Tony Kowal
askowal at northwestern.edu
Mon Dec 6 03:56:15 CET 2004
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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