[BioC] Anyone Know how to make a fake CEL file?

[Johannes Freudenberg]

Hi Richard,

> Does anyone know the corresponding i2xy function that would be needed
> for the mu72av2 chip? 

as far as I know, the i2xy() function is included in the CDF packages that you 
can download from the BioConductor website (click on MetaData). I didn't find 
the respective package for the mu72av2 chip though. I'm assuming it's something 
like

  i2xy <- function(i) cbind((i-1) %% nr, (i-1) %/% nc)

where nr is the number of rows and nc the number of columns of the chip which 
is in the case of hgu95av2:

> Dilution at nrow
[1] 640
> Dilution at ncol
[1] 640

I hope that helps,
Johannes


Quoting "Park, Richard" <Richard.Park at joslin.harvard.edu>:

> Hi Johannes,
> I am going to try and use real values from experimental cel files to
> make various fake cel files w/ varying percentages of genes changing
> over time; i.e. having 20% of the genes change w/ a 2-5 fc by the third
> time point. The point of all of this is to try and understand what
> happens during normalization. With data analyses, anywhere between 2-30,
> normalizing seems to be fine, but when you start incorporating very
> different experimental conditions in very large data groups (60+),
> normalizing seems to minimize the differences between the conditions. 
> 
> We would like to create an analysis of 100+ chips of real data to
> understand various cell  types, but with chips that are very different
> and that many different chips, normalization seems to severly limit the
> ability to see the differences between the conditions. That is why it
> would be nice to see the effects of rma (normalization and background
> correcting) and a comparison with MAS 5.0 values with spline
> normalization on a large set of "fake" cel data. 
> 
> > i2xy <- function(i) cbind((i-1) %% 640, (i-1) %/% 640) 
>   #this is for HGU-95Av2 chips
> Does anyone know the corresponding i2xy function that would be needed
> for the mu72av2 chip? 
> 
> I would appreciate any feedback from the bioconductor community. I
> haven't found anything  on the internet or literature that addresses
> this problem. 
> 
> thanks everyone, 
> Richard Park 
> 
> 
> 
> -----Original Message-----
> From: Johannes Freudenberg [mailto:mai98ftu at studserv.uni-leipzig.de]
> Sent: Tuesday, October 14, 2003 16:6 PM
> To: Park, Richard
> Subject: Re: [BioC] Anyone Know how to make a fake CEL file?
> 
> 
> Hi,
> 
> > how do you know the corresponding x and y locations on
> > the chip that correspond with the various affy ids?
> 
> The information on the probe locations is stored in the cdf environments
> and 
> can be accessed as follows:
> 
> > env <- getCdfInfo(Dilution) #get the CDF environment
> > 
> > #get the probe locations
> > loc <- apply(matrix(ls(env = env)), 1, get, env = env) 
> > 
> > #That's how it's done in S-Plus
> > #loc <- getCdfInfo(Dilution)
> > 
> > loc[[1]] # show the probe locations of the first gene
>           pm     mm
>  [1,] 175218 175858
>  [2,] 356689 357329
>  [3,] 227696 228336
>  [4,] 237919 238559
>  ...
> 
> These indices refer to the rows of the intensity matrix which is stored
> in the 
> @exprs slot of the affybatch object.  In order to get the corresponding
> x and y 
> coordinates you can use the i2xy() function:
> 
> > i2xy <- function(i) cbind((i-1) %% 640, (i-1) %/% 640) 
>   #this is for HGU-95Av2 chips
>   #corrected version, older BioC version incorrect!
>   #search BioC mailing list archive for more details
> 
> Out of curiosity, may I ask how you are going to 'fake' the different 
> treatments?  Are you using real data or simulated data?
> 
> Best wishes,
> Johannes
> 
> 
> 
> Quoting "Park, Richard" <Richard.Park at joslin.harvard.edu>:
> 
> > I am trying to make a couple of fake cel files to represent a time
> > course treatment between three time points. 
> > I am trying to test the effects of normalization on various possible
> > treatments. 
> > Is there a way to make a fake CEL file? 
> > and if there is, how do you know the corresponding x and y locations
> on
> > the chip that correspond with the various affy ids? I know that this
> > information is located in the various cdf files, but I am unaware of
> how
> > to access that information. 
> > 
> > Thanks for any help, 
> > 
> > 
> > Richard Park 
> > Immunology - Computational Data Analyzer
> > Joslin Diabetes Center
> > Ph: 617-732-2482
> > Richard.Park at joslin.harvard.edu
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> >
> 
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