[BioC] Difference in DABG between XPS package and APT

zaid haddad [guest] guest at bioconductor.org
Fri Aug 31 19:06:33 CEST 2012


I have a question regarding XPS and APT when computing DABG option.

Here's my XPS command:

#begin XPS code
dabg.call(root.data, filedir = root.path, filename = paste("tmpdt", "RMA", root.filename, sep="_"), option = "probeset", exonlevel = "all", verbose = TRUE)


Here's my APT command line:

apt-probeset-summarize -a dabg -feat-details -b /Data/affx.tech.files/HuEx-1_0-st-v2.r2/HuEx-1_0-st-v2.r2.antigenomic.bgp -p /Data/affx.tech.files/HuEx-1_0-st-v2.r2/HuEx-1_0-st-v2.r2.pgf -c /Data/affx.tech.files/HuEx-1_0-st-v2.r2/HuEx-1_0-st-v2.r2.crosshyb_1.na24.clf -s /Data/affx.tech.files/HuEx-1_0-st-v2.r2/HuEx-1_0-st-v2.r2.dt1.hg18.full.mps --qc-probesets /Data/affx.tech.files/HuEx-1_0-st-v2.r2/HuEx-1_0-st-v2.r2.qcc -o dabg/ --subsample-report --cel-files cel_list.txt


I get different p-values and different Percent Present calls. (Highly correlated though).

#R code
#[1] 0.9978199

#difference in PSRs between XPS and APT dabg output
 length(setdiff(xps.dabg[,2], rownames(apt.dabg)))
#[1] 15332
#difference in PSRs between APT and XPS dabg output
 length(setdiff( rownames(apt.dabg), xps.dabg[,2]))
#[1] 2904
#Total # of PSRs that differ
#[1] 18236
#PSRs in common
 length(intersect(xps.dabg[,2], rownames(apt.dabg)))
#[1] 1381327

The APT output is always lower in the PercentPresent.

Thanks in Advance

 -- output of sessionInfo(): 

R version 2.13.1 (2011-07-08)
Platform: x86_64-pc-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C

attached base packages:
[1] tools     splines   stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] xps_1.12.1          abind_1.4-0       survival_2.36-14
 [4] affxparser_1.24.0   fastmatch_1.0-4     glmnet_1.7.1
 [7] Matrix_0.999375-50  earth_3.2-3         plotrix_3.4-3
[10] plotmo_1.3-2        leaps_2.9           rpart_3.1-50
[13] HDclassif_1.2.1     MASS_7.3-13         randomForest_4.6-6
[16] e1071_1.6           class_7.3-3         oligo_1.14.0
[19] oligoClasses_1.14.0 frma_1.3.10         Biobase_2.12.2
[22] caret_5.15-023      cluster_1.14.0      reshape_0.8.4
[25] plyr_1.7.1          lattice_0.19-30     matrixStats_0.4.3
[28] R.methodsS3_1.4.2   abind_1.4-0         foreach_1.4.0
[31] itertools_0.1-1     iterators_1.0.5

loaded via a namespace (and not attached):
[1] affy_1.30.0           affyio_1.20.0         Biostrings_2.20.4
[4] codetools_0.2-8       DBI_0.2-5             grid_2.13.1
[7] IRanges_1.10.6        preprocessCore_1.14.0

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