Greeting ,
iam a Phd student , i try implement aroma package but its not working
with me , i don't know where is the error, and i have question the
shiptype folder is not exist be default in annotationdata, i just
create a folder in annotation data name it chiptype and i put the cdf file
in it , is that possible ??? please i need your advice this is my
program
> getwd()
[1]
"C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/ChipType"
> ChipType(""HG-U133_Plus_2")
Error: unexpected symbol in "ChipType(""HG"
> ChipType("HG-U133_Plus_2")
Error: could not find function "ChipType"
> chipType("HG-U133_Plus_2")
Error: could not find function "chipType"
> library(aroma.affymetrix)
> ChipeType("HG-U133_Plus_2")
Error: could not find function "ChipeType"
> chipType<-"HG-U133_Plus_2"
> cdf<-AffymetrixcdfFile$byChipType("HG-U133_Plus_2")
Error: object 'AffymetrixcdfFile' not found
> cdf<-AffymetrixcdfFile$bychipType("HG-U133_Plus_2")
Error: object 'AffymetrixcdfFile' not found
> cdf<-AffymetrixcdfFile$byChipType("HG-U133_Plus_2")
Error: object 'AffymetrixcdfFile' not found
> cdf<-HG-U133_Plus_2$bychipType("HG-U133_Plus_2")
Error: object 'HG' not found
> cdf<-AffymetrixcdfFile$bychipType("HG-U133_Plus_2", tags=ChipType)
Error: object 'AffymetrixcdfFile' not found
>
the error is with cdf file which can not be read
i download all the package
source("http://bioconductor.org/biocLite.R";)
biocLite("biomaRt")
hbInstall("aroma.affymetrix")
thank you
On Tuesday, April 30, 2013 8:00:45 AM UTC+1, jonathan....@mail.dcu.ie wrote:
>
> Hi Henrik,
>
> That is exactly what I was looking for. I was missing the "Order by Cell
> Indices".
> Thank you.
>
> Jonathan
>
> On Monday, April 29, 2013 11:17:57 PM UTC+2, Henrik Bengtsson wrote:
>>
>> Hi.
>>
>> On Mon, Apr 29, 2013 at 4:16 AM, <jonathan....@mail.dcu.ie> wrote:
>> > Hi Henrik,
>> >
>> > Thank you for the reply.
>> > This is quite helpful however from using the following code I am able
>> to
>> > produce a matrix of the intensities for each of the probes...
>> (replicates
>> > included)
>> >
>> > library(aroma.affymetrix)
>> > cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
>> > raw_sample <- AffymetrixCelSet$byName("Sample", cdf=cdf)
>> > ciS<- getCellIndices(cdf, unlist=TRUE, useNames=TRUE)
>> > s<- sample(ciS, 250)
>> > head(ciS)
>> > d<- extractMatrix(cs, cells=ciS, verbose=-50)
>> > write.table(file="all_probes.txt",df, quote=FALSE, sep="\t",
>> > row.names=FALSE)
>> >
>> > My issue now is that with this matrix I can see the 6+million probes
>> however
>> > the probe ID's are not present. Maybe I am missing something but If you
>> > could help me associate each probe intensity value with the probe ID I
>> would
>> > be very grateful.
>>
>> What do you mean by 'probe ID'; what you expect it do be? Note that
>> in Affymetrix terms, there are 'unit' and 'group' (probeset)
>> IDs/names, but probes don't really have IDs other that an (x,y)
>> location or an index (as you use it above).
>>
>> However, you could pull out probe-specific CDF annotation from the CDF
>> file as follows:
>>
>> library("aroma.affymetrix");
>> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
>> # Some example units
>> units <- c(1012:1013, 950123:950125);
>> # Read CDF info as data.frame
>> cdfData <- readDataFrame(cdf, units=units); # Will take a very long
>> time if done for many units
>> # Order by cell indices
>> o <- order(cdfData$cell);
>> cdfData <- cdfData[o,];
>> 'data.frame': 15 obs. of 16 variables:
>> $ unit : int 1012 1012 1013 1013 1012 1012 101..
>> $ unitType : chr "genotyping" "genotyping" "genot"..
>> $ unitType : chr "genotyping" "genotyping" "genotyping" ...
>> $ unitDirection : chr "sense" "sense" "sense" "sense" ...
>> $ unitNbrOfAtoms : int 6 6 6 6 6 6 6 6 1 1 ...
>> $ cell : int 539387 539388 902651 902652 18384..
>> $ x : int 706 707 2170 2171 2630 2631 998 9..
>> $ y : int 201 201 336 336 685 685 1112 1112..
>> $ groupNbrOfAtoms: int 3 3 3 3 3 3 3 3 1 1 ...
>> $ cell : int 539387 539388 902651 902652 ...
>> $ unit : int 1012 1012 1013 1013 1012 1012 101..
>> $ y : int 201 201 336 336 685 685 1112 1112 1195 ...
>> $ unitName : chr "SNP_A-2001598" "SNP_A-2001598" ...
>> $ unitType : chr "genotyping" "genotyping" "genot"..
>> $ indexPos : int 2 1 6 5 4 3 4 3 1 1 ...
>> $ cell : int 539387 539388 902651 902652 18384...
>>
>> # Note that for some chip types some probes (cells) occur in multiple
>> # probe sets meaning you may have duplicates. I don't think this is
>> # the case for SNP chips though. Sanity check...
>> stopifnot(!anyDuplicated(cdfData$cell));
>>
>> # Extract the corresponding probe signals from 'csR' (AffymetrixCelSet)
>> Y <- extractMatrix(csR, cells=cdfData$cell);
>>
>> # Merge CDF annotation data with signals
>> data <- cbind(cdfData, Y);
>>
>> # Save
>> # [see help("writeDataFrame.data.frame")]
>> pathname <- writeDataFrame(data, file="all_probes.txt",
>> header=list(chipType=getChipType(cdf)));
>>
>>
>> Again, not sure what you're going to use this for/where to import it;
>> you may end up reinventing the wheel.
>>
>> Hope this helps
>>
>> /Henrik
>>
>> >
>> > Thanks,
>> > Jonathan
>> >
>> > On Tuesday, April 23, 2013 2:40:56 AM UTC+2, Henrik Bengtsson wrote:
>> >>
>> >> Hi Jonathan.
>> >>
>> >> On Thu, Apr 11, 2013 at 6:38 AM, <jonathan....@mail.dcu.ie> wrote:
>> >> > Hi all,
>> >> >
>> >> > I suppose this is a simple enough task even for a newbie like me, I
>> have
>> >> > found a similar related post but I have two questions:
>> >> >
>> >> > My First Question when I use the following commands in R:
>> >> >
>> >> > library(aroma.affymetrix)
>> >> >
>> >> > cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
>> >> > cs <- AffymetrixCelSet$byName("Arles", cdf=cdf)
>> >> >
>> >> > unit <- indexOf(cdf, "SNP_A-8656720")
>> >> > y <- readUnits(cs, units=unit)
>> >> > str(y)
>> >> >
>> >> > This allows me to gather the raw intensities for a SNP or CN probe.
>> as
>> >> > follows:
>> >> > $`SNP_A-8656720`$A$intensities
>> >> > [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
>> >> > [,13]
>> >> > [,14]
>> >> > [1,] 786 807 1051 879 1971 1447 1826 236 1249 2335 1140 416
>> >> > 1147
>> >> > 2054
>> >> > [2,] 694 823 1027 835 1673 1167 1729 252 1068 2339 982 411
>> >> > 769
>> >> > 1786
>> >> > [3,] 752 665 913 820 1621 1356 1555 248 1344 2362 1417 339
>> >> > 991
>> >> > 1835
>> >> >
>> >> >
>> >> > $`SNP_A-8656720`$G
>> >> > $`SNP_A-8656720`$G$intensities
>> >> > [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
>> >> > [,13]
>> >> > [,14]
>> >> > [1,] 273 1014 481 1012 402 383 421 1138 321 861 614 1859
>> >> > 687
>> >> > 549
>> >> > [2,] 222 528 476 825 602 719 460 912 417 796 650 1617
>> >> > 537
>> >> > 661
>> >> > [3,] 259 781 543 754 492 452 550 909 316 743 518 1847
>> >> > 529
>> >> > 651
>> >> >
>> >> > From the previous post this data is supposed to reference to the A
>> and B
>> >> > allele and for the forward and reverse strands. My question is, what
>> >> > refers
>> >> > the Allele A/B ($A/$G) and forward / reverse, also by that logic
>> there
>> >> > should be 4 sets of data?
>> >>
>> >> Starting with SNP chip GenomeWideSNP_5 (sic!), Affymetrix no longer
>> >> put down probes for both strands. Instead, they pick(ed) the strand,
>> >> reverse *or* forward, that worked "the best" (the best genotyping
>> >> performance). Try this:
>> >>
>> >> > counts <- nbrOfGroupsPerUnit(cdf); # Slow first time
>> >> > table(counts);
>> >> counts
>> >> 1 2 4
>> >> 946447 906874 2748
>> >>
>> >> As you see, there are only 2,748 SNPs with both strands, whereas the
>> >> majority only have one.
>> >>
>> >> BTW, those "sets" of probes are formally referred to as "unit groups"
>> >> (it's ok to also call them "probe sets"). To find out which strands
>> >> the different unit groups are querying, you can do:
>> >>
>> >> > unit <- indexOf(cdf, "SNP_A-8656720");
>> >> > cdfList <- readUnits(cdf, units=unit);
>> >> > str(cdfList)
>> >> List of 1
>> >> $ SNP_A-8656720:List of 3
>> >> ..$ type : int 2
>> >> ..$ direction: int 2
>> >> ..$ groups :List of 2
>> >> .. ..$ A:List of 6
>> >> .. .. ..$ x : int [1:3] 1565 193 1629
>> >> .. .. ..$ y : int [1:3] 83 1466 2038
>> >> .. .. ..$ pbase : chr [1:3] "a" "a" "a"
>> >> .. .. ..$ tbase : chr [1:3] "t" "t" "t"
>> >> .. .. ..$ expos : int [1:3] 13 13 13
>> >> .. .. ..$ direction: int 2
>> >> .. ..$ G:List of 6
>> >> .. .. ..$ x : int [1:3] 1564 192 1628
>> >> .. .. ..$ y : int [1:3] 83 1466 2038
>> >> .. .. ..$ pbase : chr [1:3] "g" "g" "g"
>> >> .. .. ..$ tbase : chr [1:3] "c" "c" "c"
>> >> .. .. ..$ expos : int [1:3] 13 13 13
>> >> .. .. ..$ direction: int 2
>> >>
>> >> See that 'direction'? It specifies the strand, cf.
>> >> help("readCdfUnits", package="affxparser") [the function used
>> >> internally by readUnits()].
>> >>
>> >>
>> >> > As for CN probes this is much more obvious as there is only one
>> probe
>> >> > interrogating the position.
>> >>
>> >> Correct.
>> >>
>> >> >
>> >> > My Second Question is in relation to expanding this code in order to
>> >> > generate the raw intensities of all the SNP_ probes and then to run
>> the
>> >> > Sam
>> >> > e for CN_ probes so that I have the raw intensities for each
>> seperately?
>> >>
>> >> > types <- getUnitTypes(cdf); # Slow first time
>> >> > table(types);
>> >> types
>> >> 1 2 5
>> >> 621 909622 945826
>> >>
>> >> Here type "2" refers to a "SNP" and "5" a "CN unit". For this chip
>> >> type you could also infer which the SNPs/CN probes by their unit names
>> >> ("SNP_", and "CN_"), but that assumes that the names follow that
>> >> convention which is *not* true for other chip types. So, use
>> >> getUnitTypes():
>> >>
>> >> # SNPs
>> >> > snpUnits <- which(types == 2);
>> >> > str(snpUnits)
>> >> int [1:909622] 622 623 624 625 626 627 628 ...
>> >>
>> >> # CN probes (aka non-polymorphic loci).
>> >> > npUnits <- which(types == 5);
>> >> > str(npUnits)
>> >> int [1:945826] 910244 910245 910246 910247 ...
>> >>
>> >> Hope this helps
>> >>
>> >> /Henrik
>> >>
>> >> >
>> >> >
>> >> > Cheers,
>> >> > Jonathan
>> >> >
>> >> > --
>> >> > --
>> >> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>> >> > latest
>> >> > version of the package, 2) to report the output of sessionInfo() and
>> >> > traceback(), and 3) to post a complete code example.
>> >> >
>> >> >
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>>
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>> >> > To unsubscribe and other options, go to
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>> >> >
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>> >> >
>>
>
--
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