Dear Henrik
Meanwhile I have created ufl and ugp files for both 100K and 500K
arrays but not for GenomeWideSNP_6 aray.
Can you confirm that the following code, which I use for both 100K and
500K arrays, is correct:
# retrieving annotation files
chiptypes <- c("Mapping50K_Hind240", "Mapping50K_Xba240")
cdfs <- lapply(chiptypes, FUN=function(x){AffymetrixCdfFile$byChipType
(x)})
names(cdfs) <- chiptypes
print(cdfs)
# importing data from NetAffx CSV files
csvs <- lapply(cdfs, FUN=function(cdf){AffymetrixNetAffxCsvFile
$byChipType(getChipType(cdf), tags=".na27")})
print(csvs)
# allocating empty UFL (Unit Fragment Length) files
ufls <- lapply(cdfs, FUN=function(cdf){AromaUflFile$allocateFromCdf
(cdf, tags="na27,CS20090112")})
print(ufls)
# import SNP data
units <- list();
for (chipType in names(ufls)) {
ufl <- ufls[[chipType]];
csv <- csvs[[chipType]];
units[[chipType]] <- importFrom(ufl, csv, verbose=-50);
}
str(units)
# allocating empty UGP (Unit Genome Position) files
ugps <- lapply(cdfs, FUN=function(cdf){AromaUgpFile$allocateFromCdf
(cdf, tags="na27,CS20090112")})
print(ugps)
# import SNP data
units <- list();
for (chipType in names(ugps)) {
ugp <- ugps[[chipType]];
csv <- csvs[[chipType]];
units[[chipType]] <- importFrom(ugp, csv, verbose=-50);
}
str(units)
Here is the summary for the 100K arrays:
# Summary 50K chips
> str(units)
List of 2
$ Mapping50K_Hind240: int [1:57244] 18632 18677 1631 18713 1630 18712
18619 1639 18722 18608 ...
$ Mapping50K_Xba240 : int [1:58960] 29181 18239 31302 19831 47750
45114 19103 39711 19772 37811 ...
>
> ufl <- AromaUflFile$byChipType(chiptypes[1], tags="na27,CS20090112");
> print(summaryOfUnits(ufl, enzymes="HindIII"))
snp cnp affxSnp other total
enzyme1-only 56933 0 0 0 56933
missing 311 0 0 55 366
total 57244 0 0 55 57299
> ufl <- AromaUflFile$byChipType(chiptypes[2], tags="na27,CS20090112");
> print(summaryOfUnits(ufl, enzymes="XbaI"))
snp cnp affxSnp other total
enzyme1-only 58616 0 0 0 58616
missing 344 0 0 55 399
total 58960 0 0 55 59015
>
> ugp <- AromaUgpFile$byChipType(chiptypes[1], tags="na27,CS20090112");
> print(summary(ugp, enzymes="HindIII"))
chromosome position
Min. : 1.000 Min. : 48603
1st Qu.: 4.000 1st Qu.: 34667112
Median : 7.000 Median : 72677620
Mean : 8.402 Mean : 80405004
3rd Qu.: 12.000 3rd Qu.:114826216
Max. : 23.000 Max. :246727435
NA's :363.000 NA's : 363
> ugp <- AromaUgpFile$byChipType(chiptypes[2], tags="na27,CS20090112");
> print(summary(ugp, enzymes="XbaI"))
chromosome position
Min. : 1.000 Min. : 93683
1st Qu.: 4.000 1st Qu.: 34636629
Median : 7.000 Median : 72249739
Mean : 8.507 Mean : 80010574
3rd Qu.: 12.000 3rd Qu.:114666170
Max. : 24.000 Max. :246885089
NA's :390.000 NA's : 390
Here is the summary for the 500K arrays:
# Summary 500K chips
> str(units)
List of 2
$ Mapping250K_Sty: int [1:238304] 15133 175423 164715 237140 112643
189587 162193 79611 196992 73555 ...
$ Mapping250K_Nsp: int [1:262264] 34952 76 74370 232354 3677 72977
73533 176215 161345 238482 ...
>
> ufl <- AromaUflFile$byChipType(chiptypes[1], tags="na27,CS20090112");
> print(summaryOfUnits(ufl, enzymes="StyI"))
snp cnp affxSnp other total
enzyme1-only 144868 0 0 0 144868
missing 93436 0 0 74 93510
total 238304 0 0 74 238378
> ufl <- AromaUflFile$byChipType(chiptypes[2], tags="na27,CS20090112");
> print(summaryOfUnits(ufl, enzymes="NspI"))
snp cnp affxSnp other total
enzyme1-only 261563 0 0 0 261563
missing 701 0 0 74 775
total 262264 0 0 74 262338
>
> ugp <- AromaUgpFile$byChipType(chiptypes[1], tags="na27,CS20090112");
> print(summary(ugp, enzymes="StyI"))
chromosome position
Min. : 1.000 Min. : 2994
1st Qu.: 4.000 1st Qu.: 31306881
Median : 8.000 Median : 67082398
Mean : 9.117 Mean : 77333484
3rd Qu.: 13.000 3rd Qu.:114799352
Max. : 23.000 Max. :247135059
NA's :677.000 NA's : 677
> ugp <- AromaUgpFile$byChipType(chiptypes[2], tags="na27,CS20090112");
> print(summary(ugp, enzymes="NspI"))
chromosome position
Min. : 1.000 Min. : 17408
1st Qu.: 4.000 1st Qu.: 32574796
Median : 8.000 Median : 70596240
Mean : 8.758 Mean : 79224244
3rd Qu.: 13.000 3rd Qu.:114776300
Max. : 23.000 Max. :247110269
NA's :775.000 NA's : 775
Could it be that function summaryOfUnits() does not work as expected?
For ufl it prints "enzyme1-only" instead of e.g. "NspI-only"
For ugp it prints an error: no applicable method
Is it correct that for na27 there are now 93436 missing SNPs for StyI
compared to only 75 missing SNPs for na24 (as shown on your page about
building UFL files)?
Can I build the ufl and ugp files in the same way for GenomeWideSNP_6?
I assume that I need to repeat everything done for ".na27" with
".cn.na27"?
Will these files be identical to the files supplied by you or do you
use the file "GenomeWideSNP_6_build36_SNPandCN.tab", which only you
have (as decribed in your pages)?
Here is the sessionInfo:
> sessionInfo()
R version 2.7.1 (2008-06-23)
x86_64-unknown-linux-gnu
locale:
C
attached base packages:
[1] stats graphics grDevices datasets utils methods
base
other attached packages:
[1] aroma.affymetrix_0.9.4 aroma.apd_0.1.3
R.huge_0.1.6
[4] affxparser_1.12.2 aroma.core_0.9.4
sfit_0.1.5
[7] aroma.light_1.8.1 digest_0.3.1
matrixStats_0.1.3
[10] R.rsp_0.3.4 R.cache_0.1.7
R.utils_1.0.4
[13] R.oo_1.4.5 R.methodsS3_1.0.3
>
Best regards
Christian
On Jan 8, 2:39 pm, cstratowa <christian.strat...@vie.boehringer-
ingelheim.com> wrote:
> Dear Henrik
>
> Would it be possible for you to supply the ufl and ugp files for the
> new Affymetrix xxx.na27.annot.csv files for the mapping arrays?
>
> Thank you in advance
> Best regards
> Christian
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