Hi James,
Thanks for your reply,
I am new to R statistics.
Do I have to give the values for q or r because I am getting the following
error when I type mapply command -

Error in dimnames(x) <- dn :
  length of 'dimnames' [1] not equal to array extent

There are 5 arrays in the experiment.

Thank you,
Viritha


On Thu, Dec 16, 2010 at 11:22 AM, James W. MacDonald
<jmacdon@med.umich.edu>wrote:

> Hi Viritha,
>
>
> On 12/16/2010 10:45 AM, viritha kaza wrote:
>
>> Hi Group,
>> Let me clearly explain.I have the [Mouse430_2] Affymetrix Mouse Genome 430
>> 2.0 Array.I want to create an unnormalised expression microarray data
>> set.I
>> have the cell files and cdf file for this.I want the intensities in the
>> probe level.Is this possible in R or any other source? or how can I get
>> this
>> expression microarray dataset?
>>
>
> library(affy)
> dat <- ReadAffy()
> pms <- pm(dat, LISTRUE=TRUE)
> fun <- function(q,r){
> row.names(r) <- rep(q, ncol(r))
> r
> }
>
> pms <- mapply(fun, names(pms), pms, SIMPLIFY = FALSE)
> pms <- do.call("rbind", pms)
> write.table(pms, "Raw PM data.txt", quote = FALSE, row.names = TRUE,
> col.names = TRUE, sep = "\t")
>
> You can do similar for MM probes if you desire.
>
> Best,
>
> Jim
>
>
>
>  Thank you in advance,
>> Viritha
>>
>> On Wed, Dec 15, 2010 at 4:05 PM, viritha kaza<viritha.k@gmail.com>
>>  wrote:
>>
>> Hi group,
>>> If I want to create raw txt file of microarray data from the (affymetrix)
>>> cell file, how do I create the expression set with raw signal intensity.I
>>> know that only cell file with the version 3 can be opened as excel file
>>> as
>>> it is in ascii format.
>>> In one such cell file the intensity is indicated as:
>>>    CellHeader=X Y MEAN STDV NPIXELS 0 0 137.3 25.1 36 1 0 10730.5 2009.9
>>> 36 2 0 136.3 21.2 36
>>>         But I am not sure how to assign the probe numbers to the
>>> CellHeaders and I would also like to know if the raw intensity taken is
>>> just
>>> the mean intensity? Can this be performed in R?
>>> Waiting for your response,
>>> Thank you in advance,
>>> Viritha
>>>
>>>
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>>
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
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