[BioC] How I can extract the information of Probe and Probesets location on the microarray

[James W. MacDonald]

Hi Meiyin,

meiyin gao wrote:
> Dear List,
> 
> I have a problem.
> 
> I want to get the information about the Hgu133_Plus2 as follow,
> 
> My interest is which probes are included in each probesets? where is the
> location of these probes (x, y) in the microarray?
> 
> I know all the information are in Hgu133_Plus2 cdf file.
> 
> My problem is how I can extract these information out of this cdf file in R?
> 
> First step, like making a table:
> 
> probests1   probe1 x1  y1
>                    probe2 x2  y2
>                    probe3 x3  y3
>                    probe4 x4  y4
> ...
> ...
> probests2   probe1 x1  y1
>                    probe2 x2  y2
>                    probe3 x3  y3
>                    probe4 x4  y4
> ...
> ...
> probests54675   probe1 x1  y1
>                            probe2 x2  y2
>                            probe3 x3  y3
>                            probe4 x4  y4

How about a list instead?

 > index.list <- head(as.list(hgu133plus2cdf))
 > xy.list <- lapply(index.list, function(x) indices2xy(x[,1], 
cdf="hgu133plus2cdf"))
$`243726_at`
          x    y
  [1,]  852  919
  [2,]  895 1067
  [3,]  576  343
  [4,]  221  497
  [5,] 1101  125
  [6,]  415  915
  [7,]  981  845
  [8,]  539  239
  [9,]  755  565
[10,]  366  187
[11,]  958   27

$`1555812_a_at`
          x   y
  [1,]  702 403
  [2,]  245 159
  [3,]  817 157
  [4,]  245 801
  [5,] 1065 339
  [6,]  668 897
  [7,] 1116  87
  [8,]  360 949
  [9,]  669  69
[10,]   92 649
[11,]  265 617

$`215958_at`
          x    y
  [1,]  280  735
  [2,]   89  273
  [3,]   45 1065
  [4,] 1024 1111
  [5,]  315 1131
  [6,]  563  447
  [7,]  653  517
  [8,]   20  547
  [9,]  520   13
[10,]  624   93
[11,]  985  311

> 
> in further step, how I can extract the intensity for each probe in .cel file
> of each sample?
> probests1   probe1 x1  y1  intensity1
>                    probe2 x2  y2  intensity2
>                    probe3 x3  y3  intensity3
>                    probe4 x4  y4  intensity4

Two steps:

We need an AffyBatch first

dat <- ReadAffy()

int.data <- pm(dat, LISTRUE = TRUE, names(xy.list))

final.table <- mapply(cbind, xy.list, int.data, SIMPLIFY = FALSE)

Best,

Jim



> ...
> ...
> 
> If anyone know how I can do program in R and get this table for each sample
> (array)?
> 
> Many thanks in advance.
> 
> Bests,
> 
> Meiyin
> 
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> 
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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