[BioC] Warning on Data Entry and Failure on Normalization (marrayInput, m arrayNorm, & normalizeWithinArrays)

Fri Jun 27 16:27:20 MEST 2003

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")

names(Monkey.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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