Question: Warning on Data Entry and Failure on Normalization (marrayInput, m arrayNorm, & normalizeWithinArrays)

0

White, Charles E WRAIR-Wash DC •

**70**wrote:This is my first attempt to use a real dataset and it didn't take long
for
me to hit a wall. When I took the Bioconductor class at ENAR, I seem
to
remember something about data problems caused by investigators not
including
information they didn't use in the *.gal file. Is that my problem or
is it
something else? Code and some output are appended.
Thanks.
library(marrayInput)
Monkey.info <- read.Galfile(galfile="Revised sethi-sh 136prg.gal")
namesMonkey.info )
Monkey.info$layout
Monkey.info$gnames
> # create working dataset
> datadir <- getwd()
> fnames <- dir(path=datadir,pattern=paste("*", "gpr", sep="\."))
> Monkey<- read.GenePix(fnames, path=datadir,
+ layout = Monkey.info$layout,
+ gnames = Monkey.info$gnames)
[1] 29
[1] "Reading ....gpr"
[1] "Reading ....gpr"
[1] "Reading ....gpr"
[1] "Reading ....gpr"
[1] "Reading ....gpr"
[1] "Reading ....gpr"
[1] "Reading ....gpr"
[1] "Reading ....gpr"
[1] "Reading ....gpr"
[1] "Reading ....gpr"
[1] "Reading ....gpr"
[1] "Reading ....gpr"
[1] "Reading ....gpr"
[1] "Reading ....gpr"
[1] "Reading ....gpr"
[1] "Reading ....gpr"
[1] "Reading ....gpr"
[1] "Reading ....gpr"
[1] "Reading ....gpr"
Warning messages:
1: number of rows of result
is not a multiple of vector length (arg 2) in: cbind(Gf,
as.numeric(dat[[name.Gf]]))
2: number of rows of result
is not a multiple of vector length (arg 2) in: cbind(Gb,
as.numeric(dat[[name.Gb]]))
3: number of rows of result
is not a multiple of vector length (arg 2) in: cbind(Rf,
as.numeric(dat[[name.Rf]]))
4: number of rows of result
is not a multiple of vector length (arg 2) in: cbind(Rb,
as.numeric(dat[[name.Rb]]))
> Monkey
Pre-normalization intensity data: Object of class marrayRaw.
Number of arrays: 19 arrays.
A) Layout of spots on the array:
Array layout: Object of class marrayLayout.
Total number of spots: 15552
Dimensions of grid matrix: 12 rows by 4 cols
Dimensions of spot matrices: 18 rows by 18 cols
Currently working with a subset of 15552 spots.
Control spots:
Notes on layout:
B) Samples hybridized to the array:
Object of class marrayInfo.
Number of labels: 0
Dimensions of maInfo matrix: rows by columns
Notes:
C) Summary statistics for log-ratio distribution:
Min. 1st Qu. Median Mean 3rd Qu.
sample -8.77 -0.58 0.00 0.08 0.69
sample -8.82 -3.31 -2.32 -2.09 -1.00
sample -9.35 -1.69 -0.40 -0.39 0.89
sample -9.10 -0.02 0.74 0.82 1.62
sample -12.63 -2.10 -0.34 -0.36 1.42
sample -9.33 -2.95 -1.91 -1.80 -0.69
sample -8.74 -3.17 -2.38 -2.08 -1.10
sample -12.01 -3.58 -2.00 -2.25 -0.74
sample -8.45 -1.81 -0.85 -0.95 -0.02
sample -8.39 -2.43 -1.80 -1.83 -1.24
sample -10.34 -3.11 -2.08 -1.99 -0.93
sample -11.16 -3.21 -2.01 -2.00 -0.65
sample -8.68 -1.47 -0.84 -0.75 -0.07
sample -8.16 -1.88 -0.87 -0.95 -0.03
sample -10.97 -2.61 -1.14 -1.23 0.10
sample -7.13 -1.56 -0.66 -0.59 0.32
sample -10.86 -3.48 -2.55 -2.54 -1.57
sample -8.12 -0.35 0.21 0.28 0.85
sample -8.97 -2.58 -1.54 -1.63 -0.62
Max. NA's
sample 8.54 1714
sample 5.13 4108
sample 7.55 4514
sample 7.38 1882
sample 8.93 7030
sample 6.72 1637
sample 5.46 1670
sample 4.32 6923
sample 5.23 657
sample 4.75 829
sample 6.88 2138
sample 7.61 3924
sample 6.70 1396
sample 5.81 225
sample 6.21 2217
sample 7.67 3384
sample 7.07 3731
sample 6.84 714
sample 4.80 1343
D) Notes on intensity data:
GenePix Data
>
> library(marrayNorm)
Loading required package: stepfun
Loading required package: marrayPlots
> Monkey.norm <- maNormMain(Monkey)
Error in simpleLoess(y, x, w, span, degree, parametric, drop.square,
normalize, :
invalid `x'
>
Charles E. White, Biostatistician
Walter Reed Army Institute of Research
503 Robert Grant Ave., Room 1w102
Silver Spring, MD 20910-1557
301 319-9781
WRAIR Home Page: http://wrair-www.army.mil/
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