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

[James W. MacDonald]

On 12/16/2010 3:35 PM, viritha kaza wrote:
> Thanks James.There was no error.
> But I see that I get 11 values for the same probe.Why does it happen? If I
> perform MM as well then again I would get another file.How do I finally get
> one value for each probe in an array?

I think we need to back up a bit here. On Affy chips there are multiple 
probes used to interrogate a single transcript. As you note, for this 
particular chip there are usually 11 probes. All of the probes for a 
given transcript make up a probeset.

When we process these data, we first background correct and normalize 
the probe values to eliminate as much non-biological variability as 
possible, and then we summarize all the probes in each probeset to 
generate the final value, which we hope is proportional to the 
expression of the transcript we are trying to measure.

So we have to be precise about our terminology. You originally asked for 
a text file containing unnormalized probe values, which is what the code 
I supplied does. Evidently that is not what you wanted, so can you 
precisely state what it is that you do want?

Best,

Jim




> Thanks,
> Viritha
>
> On Thu, Dec 16, 2010 at 2:18 PM, James W. MacDonald
> <jmacdon at med.umich.edu>wrote:
>
>> 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
>>
>

-- 
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