[BioC] Imputation problem in aCGH

[Benjamin Otto]

Dear bioconductors,

Trying to impute some log2 ratios with the lowess imputation I get the
following error message, which I can't correlate with my data provided:


# Processing chromosome  2 
# Error in approx(lowess(kbl[ind], vecl[ind], f = smooth), xout = kbl[-ind])
: 
#         need at least two non-NA values to interpolate

Now here are two sets of data. The first results in the error message the
second one runs perfectly.

Set #1 (the failing one):
> mx.ratios

              X1874     X2130
AL137761  -0.104402 -0.231907
BC040221   0.520388  0.204723
NM_015677        NA  0.038293
M83653     0.133378        NA
BC033490   0.227578 -0.092427

> mx.info

              Clone Chrom     kb
AL137761   AL137761     2  29114
BC040221   BC040221     2 184720
NM_015677 NM_015677     2 219977
M83653       M83653     2 267639
BC033490   BC033490     2 270090

Set #2 (the working one):

> my.ratios

              X1874     X2130
NM_015677        NA  0.038293
M83653     0.133378        NA
BC033490   0.227578 -0.092427
AK091892  -0.177032 -0.078277
AW451118  -0.092482  0.019423

> my.info

              Clone Chrom     kb
NM_015677 NM_015677     2 219977
M83653       M83653     2 267639
BC033490   BC033490     2 270090
AK091892   AK091892     2 293681
AW451118   AW451118     2 482546


The commands used are:

> mx <- create.aCGH(mx.ratios,mx.info)
> impute.lowess(mx)

Processing chromosome  2 
Error in approx(lowess(kbl[ind], vecl[ind], f = smooth), xout = kbl[-ind]) :

        need at least two non-NA values to interpolate



SESSIONINFO:
============
R version 2.5.0 (2007-04-23) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] "tools"     "splines"   "stats"     "graphics"  "grDevices" "utils"
"datasets"  "methods"   "base"     

other attached packages:
       aCGH         sma    multtest     Biobase    survival     cluster
hgu133plus2 
   "1.10.0"    "0.5.15"    "1.14.0"    "1.14.0"      "2.31"    "1.11.5"
"1.16.0"



Has anyone an idea what the cause of the error is and why I don't get it in
the second set? I don't see any significant difference...

Best regards,

Benjamin Otto



======================================
Benjamin Otto
University Hospital Hamburg-Eppendorf
Institute For Clinical Chemistry
Martinistr. 52
D-20246 Hamburg

Tel.: +49 40 42803 1908
Fax.: +49 40 42803 4971
======================================



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