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

[James W. MacDonald]

Make that

fun <- function(q,r){
row.names(r) <- rep(q, nrow(r))
r
}

Which of course makes more sense.

Jim



On 12/16/2010 12:04 PM, viritha kaza wrote:
> 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 at 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 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
>>>>
>>>>
>>>         [[alternative HTML version deleted]]
>>>
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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
>> **********************************************************
>> Electronic Mail is not secure, may not be read every day, and should not be
>> used for urgent or sensitive issues
>>

-- 
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
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues