[BioC] Accessing SD values from CEL files

[Hooiveld, Guido]

Hi,

To follow-up on this question:
What exactely do these se (and exprs) values represent?

I am asking because when I list the 'content' of the expres and se of a
ReadAffy(sd=TRUE) object, these contain many more entries than the
number of probesets (~950,000 vs 45,101). So these are likely thus the
intesnities of individual probes. But how then to calculate the SD from
an individual probe value? (I understand this can be calculated for a
probeset, but not for a probe). 

My session for 2 arrays:

> data <- ReadAffy(sd=TRUE)
> data
AffyBatch object
size of arrays=1002x1002 features (31382 kb)
cdf=Mouse430_2 (45101 affyids)
number of samples=2
number of genes=45101
annotation=mouse4302

> exprs <- exprs(data)
> exprs
  [49984,]                               91
85
  [49985,]                              228
165
  [49986,]                              194
142
  [49987,]                              438
335
  [49988,]                              184
136
  [49989,]                              122
91
  [49990,]                               58
44
  [49991,]                              243
219
  [49992,]                              118
78
  [49993,]                               54
47
  [49994,]                               75
51
  [49995,]                               61
48
  [49996,]                              131
141
  [49997,]                               63
50
  [49998,]                              128
105
  [49999,]                               77
59
 [ reached getOption("max.print") -- omitted 954005 rows ]]

> se <- se.exprs(data)
> se
  [49984,]
13.2                                                                8.5
  [49985,]
25.3                                                               28.6
  [49986,]
27.3                                                               22.8
  [49987,]
44.5                                                               48.8
  [49988,]
32.8                                                               23.6
  [49989,]
27.1                                                               15.2
  [49990,]
10.9                                                                7.7
  [49991,]
49.6                                                               35.9
  [49992,]
15.1                                                               13.6
  [49993,]
7.6                                                                7.3
  [49994,]
11.1                                                                7.8
  [49995,]
7.6                                                                6.2
  [49996,]
24.4                                                               21.8
  [49997,]
9.5                                                                9.6
  [49998,]
24.7                                                               17.5
  [49999,]
12.5                                                               11.2
 [ reached getOption("max.print") -- omitted 954005 rows ]]
> 

Thanks for enlighten me,

Guido

 
------------------------------------------------
Guido Hooiveld, PhD
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
Wageningen University
Biotechnion, Bomenweg 2
NL-6703 HD Wageningen
the Netherlands
 
tel: (+)31 317 485788
fax: (+)31 317 483342
 
internet:   http://nutrigene.4t.com
email:      guido.hooiveld at wur.nl


> Date: Mon, 02 Apr 2007 16:21:32 -0400
> From: "James W. MacDonald" <jmacdon at med.umich.edu>
> Subject: Re: [BioC] Accessing SD values from CEL files
> To: hvanleeuwen at ucdavis.edu
> Cc: bioconductor at stat.math.ethz.ch
> Message-ID: <461165CC.5000203 at med.umich.edu>
> Content-Type: text/plain;  charset="utf-8";  format=flowed
> 
> Hi Hans,
> 
> Hans van Leeuwen wrote:
> >  
> > Hi,
> > 
> > I want to extract both the signal intensity and the 
> corresponding SD values
> > from Affymetrix CEL files. I read in the affy BioC 1.8 
> release notes that
> > ReadAffy can now optionally return the SD values stored in 
> the CEL file.
> > 
> > When I use ReadAffy I add the parameter sd = TRUE, but I am 
> trying to figure
> > out how I can get these value from the object. Is there a function,
> > equivalent to the intensities() function, to retrieve the SD values?
> 
> Yes. The function se.exprs() will do this. See 
> ?AffyBatch-class for more 
> information.
> 
> Best,
> 
> Jim
>