aroma.affymetrix 2.4.0
aroma.cn 1.0.0
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Vignette: ACNE: Allele-specific copy numbers using non-negative matrix factorization
Author: Maria Ortiz
Created on: 2009-11-18
Last updated: 2010-06-03
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This document describes how to estimate allele specific copy numbers (ASCNs) in aroma.affymetrix using ACNE (Ortiz-Estevez et al. 2010). ACNE is a summarization method that provides ASCNs. Eight (8) Affymetrix GenomeWideSNP_6 arrays deposited in NCBI-GEO under accession numbers GSE14996 (GSM374529-36) will be used to illustrate the necessary steps in aroma.affymetrix in order to apply ACNE summarization method. Note: This analysis requires the ACNE add on in addition to aroma.affymetrix. |
 Figure: Allele-specific copy numbers (CA,CB) using ACNE (left), AS-dChip (center) and AS-CRMAv2 (right) in a normal region where we know there should be three clouds located around (2,0), (1,1) and (0,2). Data is from an Mapping250K_Nsp data set. |
Setup
Annotation data
annotationData/
chipTypes/
GenomeWideSNP_6/
GenomeWideSNP_6,Full.cdf [Note: Renamed from *.Full.cdf to *,Full.cdf (w/ a comma)]
GenomeWideSNP_6,Full,na26,HB20080821.ugp
GenomeWideSNP_6,Full,na26,HB20080722.ufl
GenomeWideSNP_6,Full,HB20080710.acs
Raw data
rawData/
GSE14996,testSet/
GenomeWideSNP_6/
GSM374529.CEL, GSM374530.CEL, GSM374531.CEL, GSM374532.CEL, GSM374533.CEL, GSM374534.CEL, GSM374535.CEL, GSM374536.CEL
Analysis
Script
library("aroma.affymetrix");
library("ACNE");
verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
dataSet <- "GSE14996,testSet";
chipType <- "GenomeWideSNP_6";
# - - - - - - - - - - - - - - - - - - - - - - -
# Setup annotation data
# - - - - - - - - - - - - - - - - - - - - - - -
# Get CDF
cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full");
print(cdf);
which gives:
AffymetrixCdfFile:
Path: annotationData/chipTypes/GenomeWideSNP_6
Filename: GenomeWideSNP_6,Full.cdf
Filesize: 470.44MB
Chip type: GenomeWideSNP_6,Full
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2572x2680
Number of cells: 6892960
Number of units: 1881415
Cells per unit: 3.66
Number of QC units: 4
gi <- getGenomeInformation(cdf); print(gi);
UgpGenomeInformation:
Name: GenomeWideSNP_6
Tags: Full,na26,HB20080821
Full name: GenomeWideSNP_6,Full,na26,HB20080821
Pathname: annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na26,HB20080821.ugp
File size: 8.97 MB (9407937 bytes)
RAM: 0.00 MB
Chip type: GenomeWideSNP_6,Full
si <- getSnpInformation(cdf); print(si);
UflSnpInformation:
Name: GenomeWideSNP_6
Tags: Full,na26,HB20080722
Full name: GenomeWideSNP_6,Full,na26,HB20080722
Pathname: annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na26,HB20080722.ufl
File size: 7.18 MB (7526454 bytes)
RAM: 0.00 MB
Chip type: GenomeWideSNP_6,Full
Number of enzymes: 2
acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE)); print(acs);
AromaCellSequenceFile:
Name: GenomeWideSNP_6
Tags: Full,HB20080710
Full name: GenomeWideSNP_6,Full,HB20080710
Pathname: annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,HB20080710.acs
File size: 170.92 MB (179217531 bytes)
RAM: 0.00 MB
Number of data rows: 6892960
File format: v1
Dimensions: 6892960x26
Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw
Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
Footer: <createdOn>20080710 22:47:02 PDT</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6</chipType><srcFile><filename>GenomeWideSNP_6.probe_tab</filename><filesize>341479928</filesize><checksum>2037c033c09fd8f7c06bd042a77aef15</checksum></srcFile><srcFile2><filename>GenomeWideSNP_6.CN_probe_tab</filename><filesize>96968290</filesize><checksum>3dc2d3178f5eafdbea9c8b6eca88a89c</checksum></srcFile2>
Chip type: GenomeWideSNP_6
Platform: Affymetrix
# - - - - - - - - - - - - - - - - - - - - - - - # Setup raw data # - - - - - - - - - - - - - - - - - - - - - - - cs <- AffymetrixCelSet$byName(dataSet, cdf=cdf); print(cs);
AffymetrixCelSet:
Name: GSE14996
Tags: testSet
Path: rawData/GSE14996,testSet/GenomeWideSNP_6
Platform: Affymetrix
Chip type: GenomeWideSNP_6,Full
Number of arrays: 8
Names: GSM374529, GSM374530, ..., GSM374536
Time period: 2007-09-21 18:56:58 -- 2007-12-31 12:29:36
Total file size: 526.64MB
RAM: 0.01MB
# - - - - - - - - - - - - - - - - - - - - - - - # Probe-processing as in CRMA v2 # - - - - - - - - - - - - - - - - - - - - - - - acc <- AllelicCrosstalkCalibration(cs, model="CRMAv2"); print(acc);
AllelicCrosstalkCalibration:
Data set: GSE14996
Input tags: testSet
User tags: *
Asterisk ('*') tags: ACC,ra,-XY
Output tags: testSet,ACC,ra,-XY
Number of files: 8 (526.64MB)
Platform: Affymetrix
Chip type: GenomeWideSNP_6,Full
Algorithm parameters: (rescaleBy: chr "all", targetAvg: num 2200, subsetToAvg: chr "-XY", mergeShifts: logi TRUE, B: int 1, flavor: chr "sfit", algorithmParameters:List of 3, ..$ alpha: num [1:8] 0.1 0.075 0.05 0.03 0.01 0.0025 0.001 0.0001, ..$ q: num 2, ..$ Q: num 98)
Output path: probeData/GSE14996,testSet,ACC,ra,-XY/GenomeWideSNP_6
Is done: FALSE
RAM: 0.00MB
csC <- process(acc, verbose=verbose); print(csC);
AffymetrixCelSet:
Name: GSE14996
Tags: testSet,ACC,ra,-XY
Path: probeData/GSE14996,testSet,ACC,ra,-XY/GenomeWideSNP_6
Platform: Affymetrix
Chip type: GenomeWideSNP_6,Full
Number of arrays: 8
Names: GSM374529, GSM374530, ..., GSM374536
Time period: 2007-09-21 18:56:58 -- 2007-12-31 12:29:36
Total file size: 526.64MB
RAM: 0.01MB
bpn <- BasePositionNormalization(csC, target="zero"); print(bpn);
BasePositionNormalization:
Data set: GSE14996
Input tags: testSet,ACC,ra,-XY
User tags: *
Asterisk ('*') tags: BPN,-XY
Output tags: testSet,ACC,ra,-XY,BPN,-XY
Number of files: 8 (526.64MB)
Platform: Affymetrix
Chip type: GenomeWideSNP_6,Full
Algorithm parameters: (unitsToFit: chr "-XY", typesToFit: chr "pm", unitsToUpdate: NULL, typesToUpdate: chr "pm", shift: num 0, target: chr "zero", model: chr "smooth.spline", df: int 5)
Output path: probeData/GSE14996,testSet,ACC,ra,-XY,BPN,-XY/GenomeWideSNP_6
Is done: FALSE
RAM: 0.00MB
csN <- process(bpn, verbose=verbose); print(csN);
AffymetrixCelSet:
Name: GSE14996
Tags: testSet,ACC,ra,-XY,BPN,-XY
Path: probeData/GSE14996,testSet,ACC,ra,-XY,BPN,-XY/GenomeWideSNP_6
Platform: Affymetrix
Chip type: GenomeWideSNP_6,Full
Number of arrays: 8
Names: GSM374529, GSM374530, ..., GSM374536
Time period: 2007-09-21 18:56:58 -- 2007-12-31 12:29:36
Total file size: 526.64MB
RAM: 0.01MB
# - - - - - - - - - - - - - - - - - - - - - - - # ACNE probe summarization # - - - - - - - - - - - - - - - - - - - - - - - plm <-NmfSnpPlm(csN, mergeStrands=TRUE); print(plm);
NmfSnpPlm:
Data set: GSE14996
Chip type: GenomeWideSNP_6,Full
Input tags: testSet,ACC,ra,-XY,BPN,-XY
Output tags: testSet,ACC,ra,-XY,BPN,-XY,NMF,v4
Parameters: (probeModel: chr "pm"; shift: num 0; mergeStrands: logi TRUE).
Path: plmData/GSE14996,testSet,ACC,ra,-XY,BPN,-XY,NMF,v4/GenomeWideSNP_6
RAM: 0.00MB
if (length(findUnitsTodo(plm)) > 0) {
# Fit CN probes quickly (~5-10s/array + some overhead)
units <- fitCnProbes(plm, verbose=verbose)
str(units)
# int [1:945826] 935590 935591 935592 935593 935594 935595 ...
# Fit remaining units, i.e. SNPs (~5-10min/array)
units <- fit(plm, verbose=verbose)
str(units)
}
ces <- getChipEffectSet(plm);
print(ces);
SnpChipEffectSet:
Name: GSE14996
Tags: testSet,ACC,ra,-XY,BPN,-XY,NMF,v4
Path: plmData/GSE14996,testSet,ACC,ra,-XY,BPN,-XY,NMF,v4/GenomeWideSNP_6
Platform: Affymetrix
Chip type: GenomeWideSNP_6,Full,monocell
Number of arrays: 8
Names: GSM374529, GSM374530, ..., GSM374536
Time period: 2009-11-19 10:51:15 -- 2009-11-19 10:51:16
Total file size: 215.59MB
RAM: 0.01MB
Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE)
# - - - - - - - - - - - - - - - - - - - - - - - # Post-processing as in CRMA v2 (optional) # - - - - - - - - - - - - - - - - - - - - - - - # - - - - - - - - - - - - - - - - - - - - - - - # Extracting allele-specific CNs # - - - - - - - - - - - - - - - - - - - - - - - # Extract ASCNs for Chr2 chromosome <- 2; units <- getUnitsOnChromosome(gi, chromosome=chromosome); str(units);
int [1:153663] 26048 26049 26050 26052 26053 26054 26055 26056 26057 26058 ...
pos <- getPositions(gi, units=units); str(pos);
int [1:153663] 102496 141464 155674 160576 160616 166395 179818 179972 214086 214192 ...
# Get ASCN for sample #1 cf <- getFile(ces, 1); data <- extractTotalAndFreqB(cf, units=units); CT <- data[,"total"]; #NmfSnpPlm returns relative ASCNs (CA, CB) already standardized to the pool of all arrays. C <- CT; cn <- RawCopyNumbers(C, pos, chromosome=chromosome); print(cn);
RawCopyNumbers:
Name:
Chromosome: 2
Position range: [2785,2.42738e+08]
Number of loci: 153663
Mean distance between loci: 1579.67
Loci fields: x [153663xnumeric], y [153663xnumeric]
RAM: 1.76MB
beta <- data[,"freqB"]; fracB <- RawAlleleBFractions(beta, pos, chromosome=chromosome); print(fracB);
RawAlleleBFractions:
Name:
Chromosome: 2
Position range: [2785,2.42738e+08]
Number of loci: 153663
Mean distance between loci: 1579.67
Loci fields: x [153663xnumeric], y [153663xnumeric]
RAM: 1.76MB
# - - - - - - - - - - - - - - - - - - - - - - -
# Plot TCN and BAF
# - - - - - - - - - - - - - - - - - - - - - - -
xScale <- 1e-6;
cn <- extractSubset(cn, which(!is.na(beta))); # to erase the CN probes
subplots(2, ncol=1);
plot(cn, xScale=xScale, ylim = c(0,6), cex = .3);
stext(side=3, pos=0, getName(cn));
stext(side=3, pos=1, sprintf("Chr%d", chromosome));
plot(fracB, xScale=xScale, cex = .3, ylim = c(0,1));
References
M. Ortiz-Estevez, H. Bengtsson, A. Rubio, ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays, Bioinformatics, 2010.