Hi Emilie,
Sorry for taking such a long time to reply.
You are right: there was a bug in
AromaUnitSignalBinarySet.writeDataFrame causing the same data chunk to
be written several times. This bug will be fixed in the next realease
of aroma.core. In the meantime, Henrik has provided a patch: to
download and install it, just do
library("aroma.affymetrix");
downloadPackagePatch("aroma.core");
as (now) explained in http://aroma-project.org/howtos/updateOrPatch.
Then
dfTxt <- writeDataFrame(ds$fracB, columns=c("unitName", "chromosome",
"position", "*"))
should give you the txt file you expect. Let us know if it works for you.
Ouf !
Pierre
On Fri, Jul 2, 2010 at 6:35 AM, Emilie T <temilie...@gmail.com> wrote:
>
> Bonjour Pierre,
> Thank you for your response and and sorry for the mistake in the title of the
> subject.
> Of course my question is about the writeDataFrame() function.
> Thank you for the help on "ds" object creation. This point seems to be ok now
> but I have re-deleted the txt objects and re-try to build the txt object and
> I still have the same problem. This is very strange.
> I can see in your exemple that you also obtain duplicated rows in your
> matrix. your "d" object contain 2000000 rows and your "unique(d)"
> only 500000. Your matrix is duplicated 4 times in your case.
> Why this row duplication ?
> I see that you alo seems to use the Affy SNP 6 chip in your example. I
> suppose that we don't have the same number of raws because you certainly
> don't use the same annotation file.
> The Affy 6 SNP have about 2000000 unique unitNames (about 1M SNP + 1M CNV).
> So in your case as in mine I expect to have as unique(d) object a matrix with
> about 2M unique unitNames (or 1M if you consider that CNV units are non
> relevant for fracB calculation).
> When I compare the 'd' object unitNames to the Affy SNP 6 annotation matrix
> (see my code bellow), I see that there is several missing unitNames. In fact,
> only the first ones are presents in my "d" object.
> Do you know how to obtain the fracB measurement for this missing unitNames?
> Thank you very much for your help.
> Here is the complete code :
> > str(ds)
> List of 2
> $ total:Classes 'AromaUnitTotalCnBinarySet', 'CopyNumberDataSet',
> 'AromaUnitSignalBinarySet', 'AromaTabularBinarySet', 'GenericTabularFileSet',
> 'GenericDataFileSet', 'FullNameInterface', 'Object' atomic [1:1] NA
> .. ..- attr(*, ".env")=<environment: 0x1863b1f50>
> .. ..- attr(*, "...instantiationTime")= POSIXct[1:1], format: "2010-07-02
> 10:46:48"
> $ fracB:Classes 'AromaUnitFracBCnBinarySet', 'AromaUnitSignalBinarySet',
> 'AromaTabularBinarySet', 'GenericTabularFileSet', 'GenericDataFileSet',
> 'FullNameInterface', 'Object' atomic [1:1] NA
> .. ..- attr(*, ".env")=<environment: 0x16c5a8950>
> .. ..- attr(*, "...instantiationTime")= POSIXct[1:1], format: "2010-07-02
> 10:46:49"
> > dfTxt <- writeDataFrame(ds$fracB, columns=c("unitName", "chromosome",
> > "position", "*"))
> > d <- readDataFrame(dfTxt)
> > str(d)
> 'data.frame': 1857154 obs. of 17 variables:
> $ unitName : Factor w/ 71429 levels "AFFX-5Q-123",..: 1 2 3 4 487 490
> 493 496 499 502 ...
> $ chromosome : int NA NA NA NA NA NA NA NA NA NA ...
> $ position : int NA NA NA NA NA NA NA NA NA NA ...
> $ A,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ B,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ C,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ D,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ E,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ F,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ G,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ H,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ I,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ J,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ K,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ L,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ M,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ N,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> - attr(*, "fileHeader")=List of 6
> ..$ comments: chr "# name: data" "# tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY"
> "# fullName: data,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY" "# nbrOfFiles: 14" ...
> ..$ sep : chr "\t"
> ..$ quote : chr "\""
> ..$ skip : num 0
> ..$ topRows :List of 10
> .. ..$ : chr "unitName" "chromosome" "position" "A,fracB" ...
> .. ..$ : chr "AFFX-5Q-123" "NA" "NA" "NA" ...
> .. ..$ : chr "AFFX-5Q-456" "NA" "NA" "NA" ...
> .. ..$ : chr "AFFX-5Q-789" "NA" "NA" "NA" ...
> .. ..$ : chr "AFFX-5Q-ABC" "NA" "NA" "NA" ...
> .. ..$ : chr "AFR_A02_SB" "NA" "NA" "NA" ...
> .. ..$ : chr "AFR_A04_SB" "NA" "NA" "NA" ...
> .. ..$ : chr "AFR_A06_SB" "NA" "NA" "NA" ...
> .. ..$ : chr "AFR_A08_SB" "NA" "NA" "NA" ...
> .. ..$ : chr "AFR_A10_SB" "NA" "NA" "NA" ...
> ..$ columns : chr "unitName" "chromosome" "position" "A,fracB" ...
> > str(unique(d))
> 'data.frame': 71429 obs. of 17 variables:
> $ unitName : Factor w/ 71429 levels "AFFX-5Q-123",..: 1 2 3 4 487 490
> 493 496 499 502 ...
> $ chromosome : int NA NA NA NA NA NA NA NA NA NA ...
> $ position : int NA NA NA NA NA NA NA NA NA NA ...
> $ A,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ B,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ C,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ D,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ E,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ F,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ G,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ H,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ I,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ J,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ K,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ L,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ M,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> $ N,fracB : num NA NA NA NA NA NA NA NA NA NA ...
> - attr(*, "fileHeader")=List of 6
> ..$ comments: chr "# name: data" "# tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY"
> "# fullName: data,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY" "# nbrOfFiles: 14" ...
> ..$ sep : chr "\t"
> ..$ quote : chr "\""
> ..$ skip : num 0
> ..$ topRows :List of 10
> .. ..$ : chr "unitName" "chromosome" "position" "A,fracB" ...
> .. ..$ : chr "AFFX-5Q-123" "NA" "NA" "NA" ...
> .. ..$ : chr "AFFX-5Q-456" "NA" "NA" "NA" ...
> .. ..$ : chr "AFFX-5Q-789" "NA" "NA" "NA" ...
> .. ..$ : chr "AFFX-5Q-ABC" "NA" "NA" "NA" ...
> .. ..$ : chr "AFR_A02_SB" "NA" "NA" "NA" ...
> .. ..$ : chr "AFR_A04_SB" "NA" "NA" "NA" ...
> .. ..$ : chr "AFR_A06_SB" "NA" "NA" "NA" ...
> .. ..$ : chr "AFR_A08_SB" "NA" "NA" "NA" ...
> .. ..$ : chr "AFR_A10_SB" "NA" "NA" "NA" ...
> ..$ columns : chr "unitName" "chromosome" "position" "A,fracB" ...
>
> > unique(table(d$unitName))
> [1] 26
> As I say in my first message, I have controled wich units are missing with
> the annotation matrix :
> > ugp <- AromaUgpFile$byChipType("GenomeWideSNP_6");
> > ugp
> AromaUgpFile:
> Name: GenomeWideSNP_6
> Tags: na30,hg18,HB20100215
> Full name: GenomeWideSNP_6,na30,hg18,HB20100215
> Pathname:
> annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,na30,hg18,HB20100215.ugp
> File size: 8.85 MB (9281130 bytes)
> RAM: 0.00 MB
> Number of data rows: 1856069
> File format: v1
> Dimensions: 1856069x2
> Column classes: integer, integer
> Number of bytes per column: 1, 4
> Footer: <createdOn>20100215 21:16:37
> CET</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6</chipType><createdBy><fullname>Henrik
>
> Bengtsson</fullname><email>h...@aroma-project.org</email></createdBy><srcFiles><srcFile1><filename>GenomeWideSNP_6.cdf</filename><filesize>484489553</filesize><checksum>223f3cd9141404b2a926a40cf47d6f1a</checksum></srcFile1><srcFile2><filename>GenomeWideSNP_6,Full.cdf</filename><filesize>493291745</filesize><checksum>3fbe0f6e7c8a346105238a3f3d10d4ec</checksum></srcFile2><srcFile3><filename>GenomeWideSNP_6,Full,na30,hg18,HB20100215.ugp</filename><filesize>9407867</filesize><checksum>446e0ff43fbe9650ab48aa41ecee6bec</checksum></srcFile3></srcFiles>
> Chip type: GenomeWideSNP_6
> Platform: Affymetrix
> > ugpTxt <- writeDataFrame(ugp, columnNamesPrefix="none");
> > ugpTxt
> TabularTextFile:
> Name: GenomeWideSNP_6
> Tags: na30,hg18,HB20100215.ugp
> Full name: GenomeWideSNP_6,na30,hg18,HB20100215.ugp
> Pathname:
> annotationData,txt/GenomeWideSNP_6,na30,hg18,HB20100215/GenomeWideSNP_6/GenomeWideSNP_6,na30,hg18,HB20100215.ugp.txt
> File size: 42.17 MB (44223022 bytes)
> RAM: 0.01 MB
> Number of data rows: NA
> Columns [3]: 'unitName', 'chromosome', 'position'
> Number of text lines: NA
> > ugpdata <- readDataFrame(ugpTxt)
> > str(ugpdata)
> 'data.frame': 1856069 obs. of 3 variables:
> $ unitName : Factor w/ 1856069 levels "AFFX-5Q-123",..: 1 2 3 4 3509 3512
> 3515 3518 3521 3524 ...
> $ chromosome: int NA NA NA NA NA NA NA NA NA NA ...
> $ position : int NA NA NA NA NA NA NA NA NA NA ...
> - attr(*, "fileHeader")=List of 6
> ..$ comments: chr "# name: GenomeWideSNP_6" "# tags: na30,hg18,HB20100215"
> "# fullName: GenomeWideSNP_6,na30,hg18,HB20100215" "# sourceFile:
> GenomeWideSNP_6,na30,hg18,HB20100215.ugp" ...
> ..$ sep : chr "\t"
> ..$ quote : chr "\""
> ..$ skip : num 0
> ..$ topRows :List of 10
> .. ..$ : chr "unitName" "chromosome" "position"
> .. ..$ : chr "AFFX-5Q-123" "NA" "NA"
> .. ..$ : chr "AFFX-5Q-456" "NA" "NA"
> .. ..$ : chr "AFFX-5Q-789" "NA" "NA"
> .. ..$ : chr "AFFX-5Q-ABC" "NA" "NA"
> .. ..$ : chr "AFR_A02_SB" "NA" "NA"
> .. ..$ : chr "AFR_A04_SB" "NA" "NA"
> .. ..$ : chr "AFR_A06_SB" "NA" "NA"
> .. ..$ : chr "AFR_A08_SB" "NA" "NA"
> .. ..$ : chr "AFR_A10_SB" "NA" "NA"
> ..$ columns : chr "unitName" "chromosome" "position"
> > common <- ugpdata$unitName %in% d$unitName
> > plot(as.numeric(common),xlim=c(1,length(common)),ylim=c(0,1))
>
>
> 2010/7/2 Pierre Neuvial <pie...@stat.berkeley.edu>
>>
>> Salut Emilie,
>>
>> On Thu, Jul 1, 2010 at 10:13 AM, EmilieT <temilie...@gmail.com> wrote:
>> > Hello,
>> >
>> > I am using your R framework with a set of Affymetrix SNP 6 data and I
>> > have a problem with the extractDataFrame function.
>> > The result is an incomplete matrix with row duplication.
>> >
>> >> sessionInfo()
>> > R version 2.11.1 (2010-05-31)
>> > x86_64-apple-darwin9.8.0
>> >
>> > locale:
>> > [1] fr_FR.UTF-8/fr_FR.UTF-8/C/C/fr_FR.UTF-8/fr_FR.UTF-8
>> >
>> > attached base packages:
>> > [1] stats graphics grDevices utils datasets methods
>> > base
>> >
>> > other attached packages:
>> > [1] aroma.cn_0.5.0 aroma.affymetrix_1.6.0
>> > aroma.apd_0.1.7 affxparser_1.20.0 R.huge_0.2.0
>> > [6] aroma.core_1.6.0 matrixStats_0.2.1
>> > R.rsp_0.3.6 R.cache_0.3.0 R.filesets_0.8.2
>> > [11] digest_0.4.2 R.utils_1.4.0
>> > R.oo_1.7.2 aroma.light_1.16.0 R.methodsS3_1.2.0
>> >
>> > I use the standard doCRMAv2 function :
>> > > ds <- doCRMAv2("data",
>> > chipType="GenomeWideSNP_6",combineAlleles=FALSE);
>> >
>> >> ds
>> > $total
>> > AromaUnitTotalCnBinarySet:
>> > Name: data
>> > Tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
>> > Full name: data,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
>> > Number of files: 14
>> > Names: A,B, ..., C [14]
>> > Path (to the first file): totalAndFracBData/data,ACC,ra,-XY,BPN,-
>> > XY,AVG,FLN,-XY/GenomeWideSNP_6
>> > Total file size: 99.13 MB
>> > RAM: 0.02MB
>> >
>> > $fracB
>> > AromaUnitFracBCnBinarySet:
>> > Name: data
>> > Tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
>> > Full name: data,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
>> > Number of files: 14
>> > Names: A,B, ..., C [14]
>> > Path (to the first file): totalAndFracBData/data,ACC,ra,-XY,BPN,-
>> > XY,AVG,FLN,-XY/GenomeWideSNP_6
>> > Total file size: 99.13 MB
>> > RAM: 0.02MB
>> >
>> > It seems to be impossible to use this 'ds' object (or ds$fracB or ds
>> > $total) as an entrance for the extractDataFrame() function.
>>
>> Yes: this is because extractDataFrame is meant to extract *chip
>> effects* (http://aroma-project.org/howtos/extractDataFrame) in your
>> case total and allele-specific *intensities*, and your ds$total and
>> ds$fracB are already one step further in the analysis: they are
>> AromaUnit*CnBinaryFile:s. For these you can use writeDataFrame
>> (http://aroma-project.org/howtos/writeDataFrame) as you seem to be
>> doing below.
>>
>> > So I must do :
>> >
>> >> rootPath <- "totalAndFracBData"
>> >> dataSet <- "data,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY"
>> >> ds <- AromaUnitFracBCnBinarySet$byName(dataSet,
>> >> chipType="GenomeWideSNP_6", paths=rootPath);
>> >> ds
>> > AromaUnitFracBCnBinarySet:
>> > Name: data
>> > Tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
>> > Full name: data,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
>> > Number of files: 14
>> > Names: A,B, ..., C [14]
>> > Path (to the first file): totalAndFracBData/data,ACC,ra,-XY,BPN,-
>> > XY,AVG,FLN,-XY/GenomeWideSNP_6
>> > Total file size: 99.13 MB
>> > RAM: 0.02MB
>>
>> You don't really to do this: your new 'ds' is exactly your previous
>> 'ds$fracB' (more on this below).
>>
>> >
>> > When I use the extractDataFrame function, I obtain the folowing
>> > object :
>>
>> Below you are using writeDataFrame, not extractDataFrame. Right ?
>>
>> >
>> >> dfTxt <- writeDataFrame(ds, columns=c("unitName", "chromosome",
>> >> "position", "*"))
>> >> d <- readDataFrame(dfTxt)
>> >> str(d)
>> > 'data.frame': 1857154 obs. of 17 variables:
>> > $ unitName : Factor w/ 71429 levels
>> > "AFFX-5Q-123",..: 1 2 3 4 487 490 493 496 499 502 ...
>> > $ chromosome : int NA NA NA NA NA NA NA NA NA NA ...
>> > $ position : int NA NA NA NA NA NA NA NA NA
>> > NA ...
>> > $ A,fracB : num NA NA NA NA NA NA NA NA NA
>> > NA ...
>> > $ B,fracB : num NA NA NA NA NA NA NA NA NA
>> > NA ...
>> > $ C,fracB : num NA NA NA NA NA NA NA NA NA
>> > NA ...
>> > $ ...
>> >
>> > First of all, you can see that there is only the fracB columns. The
>> > first "ds" object had a "total" item, it seems to have been lost. The
>> > directory
>> > /totalAndFracBData/data,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY/GenomeWideSNP_6
>> > also contain the ....,total.asb files. There is maybe a problem with
>> > my new 'ds' object (which refers to only 14 files).
>>
>> Yes, this is expected because your new 'ds' has been created using
>>
>> ds <- AromaUnitFracBCnBinarySet$byName(dataSet,
>> chipType="GenomeWideSNP_6", paths=rootPath);
>>
>> As the "FracB" indicates, this 'ds' only contains allele B fractions. You
>> can do
>>
>> totalDs <- AromaUnitTotalCnBinarySet$byName(dataSet,
>> chipType="GenomeWideSNP_6", paths=rootPath);
>>
>> to get the corresponding total CN data.
>>
>> >
>> > There is also a problem of row duplication : you can see that the
>> > number of row is the same as Affymetrix SNP 6 number of units (so the
>> > result seems to be good).
>>
>> Well, I've tried to reproduce what you have and I'm getting 2000000 rows:
>>
>> > str(d);
>> 'data.frame': 2000000 obs. of 5 variables:
>> $ unitName : Factor
>> w/ 500000 levels "AFFX-5Q-123",..: 1 2 3 4 487 490 493 496 499 502 ...
>> $ chromosome : int
>> NA NA NA NA NA NA NA NA NA NA ...
>> $ position : int
>> NA NA NA NA NA NA NA NA NA NA ...
>> $ STAIR_p_TCGA_Batch7_Affx_N_GenomeWideSNP_6_E03_238454,fracB: num
>> NA NA NA NA NA NA NA NA NA NA ...
>> $ STAIR_p_TCGA_Batch7_Affx_N_GenomeWideSNP_6_E04_238456,fracB: num
>> NA NA NA NA NA NA NA NA NA NA ...
>> - attr(*, "fileHeader")=List of 6
>> ..$ comments: chr "# name: TumorBoostPaper" "# tags:
>> pairs,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY" "# fullName:
>> TumorBoostPaper,pairs,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY" "# nbrOfFiles:
>> 2" ...
>> ..$ sep : chr "\t"
>> ..$ quote : chr "\""
>> ..$ skip : num 0
>> ..$ topRows :List of 10
>> .. ..$ : chr "unitName" "chromosome" "position"
>> "STAIR_p_TCGA_Batch7_Affx_N_GenomeWideSNP_6_E03_238454,fracB" ...
>> .. ..$ : chr "AFFX-5Q-123" "NA" "NA" "NA" ...
>> .. ..$ : chr "AFFX-5Q-456" "NA" "NA" "NA" ...
>> .. ..$ : chr "AFFX-5Q-789" "NA" "NA" "NA" ...
>> .. ..$ : chr "AFFX-5Q-ABC" "NA" "NA" "NA" ...
>> .. ..$ : chr "AFR_A02_SB" "NA" "NA" "NA" ...
>> .. ..$ : chr "AFR_A04_SB" "NA" "NA" "NA" ...
>> .. ..$ : chr "AFR_A06_SB" "NA" "NA" "NA" ...
>> .. ..$ : chr "AFR_A08_SB" "NA" "NA" "NA" ...
>> .. ..$ : chr "AFR_A10_SB" "NA" "NA" "NA" ...
>> ..$ columns : chr "unitName" "chromosome" "position"
>> "STAIR_p_TCGA_Batch7_Affx_N_GenomeWideSNP_6_E03_238454,fracB" ...
>>
>> > But there is only 71429 unique unitNames. In
>> > fact, there is only 71429 unique rows :
>> >
>> >> str(unique(d))
>> > 'data.frame': 71429 obs. of 17 variables:
>> > $ unitName : Factor w/ 71429 levels "AFFX-5Q-123",..: 1
>> > 2 3 4 487 490 493 496 499 502 ...
>> > $ chromosome : int NA NA NA NA NA NA NA NA NA NA ...
>> > $ position : int NA NA NA NA NA NA NA NA NA NA ...
>> > $ A,fracB : num NA NA NA NA NA NA NA NA NA NA ...
>> > $ B,fracB : num NA NA NA NA NA NA NA NA NA NA ...
>> > $ C,fracB : num NA NA NA NA NA NA NA NA NA NA ...
>> > $ ...
>> >
>> > Each row seems to be duplicated 26 times :
>> >> unique(table(d$unitName))
>> > [1] 26
>> >
>>
>> I can't reproduce this. Here is what I get:
>>
>> > str(unique(d))
>> 'data.frame': 500000 obs. of 5 variables:
>> $ unitName : Factor
>> w/ 500000 levels "AFFX-5Q-123",..: 1 2 3 4 487 490 493 496 499 502 ...
>> $ chromosome : int
>> NA NA NA NA NA NA NA NA NA NA ...
>> $ position : int
>> NA NA NA NA NA NA NA NA NA NA ...
>> $ STAIR_p_TCGA_Batch7_Affx_N_GenomeWideSNP_6_E03_238454,fracB: num
>> NA NA NA NA NA NA NA NA NA NA ...
>> $ STAIR_p_TCGA_Batch7_Affx_N_GenomeWideSNP_6_E04_238456,fracB: num
>> NA NA NA NA NA NA NA NA NA NA ...
>> - attr(*, "fileHeader")=List of 6
>> ..$ comments: chr "# name: TumorBoostPaper" "# tags:
>> pairs,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY" "# fullName:
>> TumorBoostPaper,pairs,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY" "# nbrOfFiles:
>> 2" ...
>> ..$ sep : chr "\t"
>> ..$ quote : chr "\""
>> ..$ skip : num 0
>> ..$ topRows :List of 10
>> .. ..$ : chr "unitName" "chromosome" "position"
>> "STAIR_p_TCGA_Batch7_Affx_N_GenomeWideSNP_6_E03_238454,fracB" ...
>> .. ..$ : chr "AFFX-5Q-123" "NA" "NA" "NA" ...
>> .. ..$ : chr "AFFX-5Q-456" "NA" "NA" "NA" ...
>> .. ..$ : chr "AFFX-5Q-789" "NA" "NA" "NA" ...
>> .. ..$ : chr "AFFX-5Q-ABC" "NA" "NA" "NA" ...
>> .. ..$ : chr "AFR_A02_SB" "NA" "NA" "NA" ...
>> .. ..$ : chr "AFR_A04_SB" "NA" "NA" "NA" ...
>> .. ..$ : chr "AFR_A06_SB" "NA" "NA" "NA" ...
>> .. ..$ : chr "AFR_A08_SB" "NA" "NA" "NA" ...
>> .. ..$ : chr "AFR_A10_SB" "NA" "NA" "NA" ...
>> ..$ columns : chr "unitName" "chromosome" "position"
>> "STAIR_p_TCGA_Batch7_Affx_N_GenomeWideSNP_6_E03_238454,fracB" ...
>>
>> >
>> > I use the extractDataFrame function on the ugp object and it seems to
>> > work so my ugp file is probably correct.
>>
>> What have you done exactly here ?
>>
>> > I also notice that the 71429 unitNames of the 'd' object are the first
>> > 71429 lines of my ugp matrix.
>> >
>>
>> Can you delete the txt file and (re)do
>>
>> ds <- doCRMAv2("data", chipType="GenomeWideSNP_6",combineAlleles=FALSE);
>> dfTxt <- writeDataFrame(ds$fracB, columns=c("unitName", "chromosome",
>> "position", "*"))
>> d <- readDataFrame(dfTxt)
>>
>> ? Do you stil have the same problem ?
>>
>> Pierre
>>
>> > I hope you can help me out. Thank you
>> >
>> > --
>> > 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.
>> >
>> >
>> > You received this message because you are subscribed to the Google Groups
>> > "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> > To post to this group, send email to aroma-affymetrix@googlegroups.com
>> > To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>> >
>>
>> --
>> 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.
>>
>>
>> You received this message because you are subscribed to the Google Groups
>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> To post to this group, send email to aroma-affymetrix@googlegroups.com
>> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> --
> 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.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
--
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.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
