[BioC] Conversion of affymetrix cell file to raw text file

[James W. MacDonald]

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 at 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.
Ann Arbor MI 48109-5618
734-615-7826
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