[BioC] affyxparser package question

Benilton Carvalho bcarvalh at jhsph.edu
Thu Aug 9 08:50:59 CEST 2007 

try:

  dbGetQuery(db(pd.mapping50k.xba240), "SELECT * FROM sequence LIMIT 5")

and let us know if that contains what you expected.

b

On Aug 8, 2007, at 7:04 PM, Tae-Hoon Chung wrote:

> Hi, Benilton;
>
> I can understand what you mean. Basically, information from  
> read.celfiles() is equivalent with that from readCelUnits() except  
> the necessary transformation from list to vectors to make a  
> SnpFeatureSet object. Obviously, the forward/backward strand  
> information can be retrieved from the annotation package. Still,  
> there's no indication which values are for central probes and which  
> values are for shifted probes, right? When I looked at the  
> annotation package, it contained the following information: fid,  
> strand, allele, fsetid, pos, x, y. It seemed like the "pos"  
> information was somehow related to central/shifted probes but was  
> not clear.
>
> 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 3:43 PM, Benilton Carvalho wrote:
>
>> What happens is pretty the same effect of what you get when you do  
>> as.numeric() on a matrix...
>>
>> There is a one to one mapping between X and Y coordinates (given  
>> that you the dimensions of the chip) to an index... This is the  
>> nature of the xy2i function used a lot on the affy package and  
>> everything else on BioConductor. And that's how we get the vector.
>>
>> The basic idea behind the CEL file (over-simplifying here) is that  
>> it contains 3 columns that we use and I could mimic it with  
>> something like:
>>
>> ints <- rnorm(80)
>> fake.cel <- expand.grid(X=1:10, Y=1:8)
>> fake.cel <- cbind(fake.cel, intensity=ints)
>>
>> if you have a few minutes, you'll see that there is an association  
>> between the X and Y columns with the rownumber... this rownumber  
>> is the "index" I referred to above and is the "fid" column in the  
>> annotation.
>>
>> b
>>
>> On Aug 8, 2007, at 6:33 PM, Tae-Hoon Chung wrote:
>>
>>> 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
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> 	[[alternative HTML version deleted]]
>>>>>>>
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>>>>>
>>>
>

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