[BioC] affyxparser package question

[Benilton Carvalho]

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
>>>
>>>
>>>
>>> 	[[alternative HTML version deleted]]
>>>
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>