Dear List, 

 

            I am a newcomer to R and an absolute rank rookie with
Bioconductor and microarray analysis.  I am trying to find the gene
expression summary values in the Dilution data set.  I am working
through the 2nd chapter of the book by Gentlemen, Carey, Huber, Irizarry
and Dudoit (BACBSURAB).  My question is simple: Have I obtained the
matrix/data frame containing the summary expression values after
correcting for background (convolution method), normalizing (quantile
method) using the rma function?  Many thanks.

 

Here are the commands:

 

> library('affy') 

Loading required package: Biobase

Loading required package: tools

 

Welcome to Bioconductor 

 

        Vignettes contain introductory material.

        To view, simply type 'openVignette()' or start with
'help(Biobase)'. 

        For details on reading vignettes, see the openVignette help
page.

 

> library('affydata') 

> data(Dilution) 

> eset <- rma(Dilution) 

Background correcting

Normalizing

Calculating Expression

> attributes.eset <- attributes(eset) 

> names(attributes.eset) 

[1] "exprs"        "se.exprs"     "description"  "annotation"   "notes"


[6] "reporterInfo" "phenoData"    "class"       

> eset.exprs <- attributes.eset$exprs

> eset.exprs.df <- data.frame(eset.exprs)

> dim(eset.exprs.df) 

[1] 12625     4 

> summary(eset.exprs.df) 

      X20A             X20B             X10A             X10B       

 Min.   : 2.266   Min.   : 2.220   Min.   : 2.239   Min.   : 2.246  

 1st Qu.: 4.725   1st Qu.: 4.689   1st Qu.: 4.727   1st Qu.: 4.697  

 Median : 6.229   Median : 6.210   Median : 6.233   Median : 6.215  

 Mean   : 6.190   Mean   : 6.178   Mean   : 6.191   Mean   : 6.183  

 3rd Qu.: 7.519   3rd Qu.: 7.513   3rd Qu.: 7.514   3rd Qu.: 7.528  

 Max.   :13.402   Max.   :13.403   Max.   :13.443   Max.   :13.489      

> eset.exprs.df[1:3,] 

             X20A     X20B     X10A     X10B

100_g_at 8.039951 7.891520 8.022282 7.910679

1000_at  7.790855 7.661225 7.716811 7.622734

1001_at  5.175568 5.067023 5.082672 5.091804

 

Is this data frame, eset.exprs.df, that contains the summary expression
values after correcting for background (convolution method), normalizing
(quantile method) using the rma function?

 

Thank you very much,

 

            Greg 

 

W. Gregory Alvord, Ph.D.

Director, Statistical Consulting Services

Computer and Statistical Services

National Cancer Institute at Frederick

Fort Detrick at 7th Street

Post Office Box B

Miller Drive, Building 362, Room 33

Frederick, MD  21702-1201

Phone:  301.846.5101

Fax:  301.846.6196

E-mail:  gwa@css.ncifcrf.gov

 


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