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.
>
>
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>
--
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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