Question: Warning on Data Entry and Failure on Normalization (marrayInput, m arrayNorm, & normalizeWithinArrays)
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16.4 years ago by
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/ [[alternative HTML version deleted]]
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