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]] >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioconductor mailing list >>>>>>> Bioconductor at stat.math.ethz.ch >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>> Search the archives: http://news.gmane.org/ >>>>>>> gmane.science.biology.informatics.conductor >>>>> >>> >