Hi, Benilton;

When I tried the 'low-level' method of using readCelUnits(), I got a  
list with individual probe intensities. However, when I tried  
read.celfiles() from 'oligo' package, I got an object of  
'SnpFeatureSet' class whose measurement values were retrieved through  
exprs() method. However, the matrix retrieved by this method  
contained one vector for each sample and it was hard to figure out  
how the low-level intensity values were transformed into a single  
vector. I am curious if the low-level intensity values are still  
preserved in the SnpFeatureSet object or more or less summarized in it.

Tae-Hoon Chung

Post-Doctoral Researcher
Computational Biology Division, TGEN
445 N 5th St. Phoenix, AZ 85004 USA
O: 1-602-343-8724
F: 1-602-343-8840


On Aug 8, 2007, at 3:24 PM, Benilton Carvalho wrote:

> I don't mean that it's going to be very hard.... I mean that it  
> might give you some work and someone else already figured that out  
> for you and you could have been using your time for something else.
>
> All you need is something like:
>
> library(pd.mapping50k.xba240)
> dbGetQuery(db(pd.mapping50k.xba240), "SELECT * from pmfeature LIMIT  
> 5")
>
> b
>
> On Aug 8, 2007, at 6:15 PM, Tae-Hoon Chung wrote:
>
>> Hi, Benilton;
>>
>> Does this mean that it's going to be tough to tell which ones are  
>> for forward/backward strand or for central/shifted probe without  
>> involving annotation package?
>>
>> Tae-Hoon Chung
>>
>> Post-Doctoral Researcher
>> Computational Biology Division, TGEN
>> 445 N 5th St. Phoenix, AZ 85004 USA
>> O: 1-602-343-8724
>> F: 1-602-343-8840
>>
>>
>> On Aug 8, 2007, at 3:08 PM, Benilton Carvalho wrote:
>>
>>> any specific reason to not use
>>>
>>> library(oligo)
>>> x = read.celfiles(list.celfiles())
>>>
>>> and check the annotation packages?
>>>
>>> b
>>>
>>> On Aug 8, 2007, at 6:02 PM, Tae-Hoon Chung wrote:
>>>
>>>> Hi;
>>>>
>>>> When one uses readCelUnits() to read SNP chip cel files, how one  
>>>> can
>>>> tell which values are for forward strand or for backward strand and
>>>> which values are from the non-shifted probes or from the shifted
>>>> probes? For instance, in the following code chunk, which values are
>>>> from forward/backward strand and from central/shifted probes?
>>>>
>>>> library("hapmap100kxba", lib="~/Library/R64")
>>>> library(affxparser, lib="~/Library/R64")
>>>>
>>>> pth <- system.file('celFiles', package='hapmap100kxba')
>>>> files <- list.files(path=pth, full.names=T)
>>>>
>>>> chip.type <- readCelHeader(files[1])$chiptype  ## Mapping50K_Xba240
>>>> cels <- readCelUnits(files[1], cdf='~/Project/ProbeAnnot/
>>>> Mapping50K_Xba240.cdf', stratifyBy='pm', addDimnames=T)
>>>> length(cels)  ## 59015
>>>> labs.test <- names(cels)[100:120]
>>>> cels[[labs.test[1]]]
>>>> ## $A
>>>> ## $A$intensities
>>>> ## [1]  7563  8050  9531  9292 11261
>>>> ##
>>>> ## $G
>>>> ## $G$intensities
>>>> ## [1]  6540  7639  9027 10512 11381
>>>> ##
>>>> ## $A
>>>> ## $A$intensities
>>>> ## [1] 4036 4144 3858 5170 3975
>>>> ##
>>>> ## $G
>>>> ## $G$intensities
>>>> ## [1] 4425 4291 3682 5912 5208
>>>>
>>>>
>>>> Tae-Hoon Chung
>>>>
>>>> Post-Doctoral Researcher
>>>> Computational Biology Division, TGEN
>>>> 445 N 5th St. Phoenix, AZ 85004 USA
>>>> O: 1-602-343-8724
>>>> F: 1-602-343-8840
>>>>
>>>>
>>>>
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>>>>
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