One-factorial ANOVA assessing pin-dependent bias.

Description

This function performs an one-factorial analysis of variance assessing microtiter plate-dependent bias for a single array

Usage

anovaplate(obj,index)

Arguments

Details

The function anovapin performs a one-factorial ANOVA for objects of class “marrayRaw” or “marrayNorm”. The predictor variable is the corresponding plate index as stored in the maPlate slot of obj; the response variable is the logged fold-change M=(log2(Ch2)-log2(Ch1)). The null hypothesis is equal mean(M) of groups of spots derived from the same microtiter plate i.e. a spot's M does not dependent on the plate of origin. The model formula used is M ~ (plate.index - 1) (without an intercept term).

Value

The return value is a list of summary statistics of the fitted model as produced by summary.lm. For example, the squared multiple correlation coefficient R-square equals the proportion of the variation of M that can be explained by the variation of plate index (based on the chosen ANOVA model.)

Author(s)

Matthias E. Futschik (http://itb.biologie.hu-berlin.de/~futschik)

See Also

anova, summary.lm

Examples

# CHECK RAW DATA FOR INTENSITY-DEPENDENT BIAS
data(sw)
print(anovapin(sw,index=1))


# CHECK  DATA NORMALISED BY OLIN FOR INTENSITY-DEPENDENT BIAS
data(sw.olin)
print(anovapin(sw.olin,index=1))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(OLIN)
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: marray
Loading required package: limma
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/OLIN/anovaplate.Rd_%03d_medium.png", width=480, height=480)
> ### Name: anovaplate
> ### Title: One-factorial ANOVA assessing pin-dependent bias.
> ### Aliases: anovaplate
> ### Keywords: models regression
> 
> ### ** Examples
> 
> 
> # CHECK RAW DATA FOR INTENSITY-DEPENDENT BIAS
> data(sw)
> print(anovapin(sw,index=1))

Call:
lm(formula = M ~ pin - 1)

Residuals:
    Min      1Q  Median      3Q     Max 
-3.2115 -0.3006 -0.0023  0.2893  2.7091 

Coefficients:
      Estimate Std. Error t value Pr(>|t|)    
pin1  -0.82109    0.03005 -27.328  < 2e-16 ***
pin2  -0.63777    0.03005 -21.227  < 2e-16 ***
pin3  -0.11633    0.03005  -3.872 0.000110 ***
pin4   0.03448    0.03005   1.148 0.251226    
pin5  -0.41337    0.03005 -13.758  < 2e-16 ***
pin6  -0.42165    0.03005 -14.034  < 2e-16 ***
pin7  -0.18132    0.03005  -6.035 1.73e-09 ***
pin8  -0.11484    0.03005  -3.822 0.000134 ***
pin9   0.07658    0.03005   2.549 0.010845 *  
pin10 -0.03252    0.03005  -1.082 0.279108    
pin11 -0.03955    0.03005  -1.316 0.188128    
pin12 -0.09613    0.03005  -3.200 0.001387 ** 
pin13  0.78404    0.03005  26.095  < 2e-16 ***
pin14  0.62758    0.03005  20.888  < 2e-16 ***
pin15  0.57510    0.03005  19.141  < 2e-16 ***
pin16  0.33686    0.03005  11.212  < 2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.4882 on 4208 degrees of freedom
Multiple R-squared:  0.438,	Adjusted R-squared:  0.4359 
F-statistic:   205 on 16 and 4208 DF,  p-value: < 2.2e-16

> 
> 
> # CHECK  DATA NORMALISED BY OLIN FOR INTENSITY-DEPENDENT BIAS
> data(sw.olin)
> print(anovapin(sw.olin,index=1))

Call:
lm(formula = M ~ pin - 1)

Residuals:
    Min      1Q  Median      3Q     Max 
-3.2696 -0.1682  0.0088  0.1802  2.5332 

Coefficients:
        Estimate Std. Error t value Pr(>|t|)
pin1   0.0062797  0.0237020   0.265    0.791
pin2  -0.0241356  0.0237020  -1.018    0.309
pin3   0.0107550  0.0237020   0.454    0.650
pin4   0.0092225  0.0237020   0.389    0.697
pin5   0.0053570  0.0237020   0.226    0.821
pin6  -0.0196653  0.0237020  -0.830    0.407
pin7   0.0161159  0.0237020   0.680    0.497
pin8  -0.0063346  0.0237020  -0.267    0.789
pin9   0.0071868  0.0237020   0.303    0.762
pin10  0.0063985  0.0237020   0.270    0.787
pin11  0.0108643  0.0237020   0.458    0.647
pin12  0.0037059  0.0237020   0.156    0.876
pin13  0.0073112  0.0237020   0.308    0.758
pin14 -0.0170648  0.0237020  -0.720    0.472
pin15 -0.0143591  0.0237020  -0.606    0.545
pin16 -0.0008543  0.0237020  -0.036    0.971

Residual standard error: 0.3851 on 4208 degrees of freedom
Multiple R-squared:  0.0009778,	Adjusted R-squared:  -0.002821 
F-statistic: 0.2574 on 16 and 4208 DF,  p-value: 0.9987

> 
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> dev.off()
null device 
          1 
>