[BioC] Trying to find the expression summary values

[James W. MacDonald]

Hi Greg,

Alvord, Greg (DMS) [Contr] wrote:
> 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?

Yes, but note that the canonical method to get these data is to use the 
exprs() accessor. In this case you would do:

eset.exprs.df <- exprs(eset)

by using the accessor functions you are protected from any underlying 
changes that may have been made to the package.

HTH,

Jim

> 
>  
> 
> 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 at css.ncifcrf.gov
> 
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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