Dear Aroma.affymetrix teem, I followed the vignette "Allele-specific copy numbers using non-negative matrix factorization". I want to extract LRR and BAF to feed into another software "ASCAT <http://heim.ifi.uio.no/bioinf/Projects/ASCAT/>" to correct aneuploidy and normal contamination.
>From the vignette, I can use extractTotalAndFreqB to extract total CN and BAF. My question is how can I get LRR from Total CN. I went through this thread "creat binary data files containing BAF data <https://groups.google.com/forum/#!searchin/aroma-affymetrix/kai/aroma-affymetrix/1Qcj_nxiQvc/ViKo4wnWcvwJ>", but get confused. quote from "creat binary data files containing BAF data <https://groups.google.com/forum/#%21searchin/aroma-affymetrix/kai/aroma-affymetrix/1Qcj_nxiQvc/ViKo4wnWcvwJ> " "The take-home message is that the definition of "log2 ratios" has become de facto standard in our field, where as "CN" is a bit ambiguous, and can mean "CN ratio" (C=theta/thetaR, or C=2*theta/thetaR) as well as "CN intensity" (theta). By adding tags we try to make this less ambiguous." How total CN was defined in aroma.affymetrix? Best regards, Hongen my code ############ library("aroma.affymetrix") library("ACNE") log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE) # Don't display too many decimals. options(digits=4) #Verifying annotation data files cdf <- AffymetrixCdfFile$byChipType("CytoScanHD_Array"); print(cdf) gi <- getGenomeInformation(cdf) print(gi) si <- getSnpInformation(cdf) print(si) acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE)) print(acs) ##raw data sets csR<- AffymetrixCelSet$byName("smida", cdf=cdf); ###step 1 Calibration for crosstalk between allele probe pairs acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2") print(acc) csC <- process(acc, verbose=verbose) print(csC) ##Step 2 - Normalization for nucleotide-position probe sequence effects bpn <- BasePositionNormalization(csC, target="zero") csN <- process(bpn, verbose=verbose) cs <- csN #step 3 #Probe summarization using non-negative-matrix factorization (NMF) plm <- NmfSnpPlm(csN, mergeStrands=TRUE) print(plm) 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) my session information: ###################### > sessionInfo() R version 3.1.3 (2015-03-09) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: Fedora 20 (Heisenbug) locale: [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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ACNE_0.8.0 aroma.light_2.2.1 aroma.affymetrix_2.13.2 [4] aroma.core_2.13.1 R.devices_2.13.0 R.filesets_2.7.2 [7] R.utils_2.0.2 R.oo_1.19.0 affxparser_1.38.0 [10] R.methodsS3_1.7.0 loaded via a namespace (and not attached): [1] aroma.apd_0.6.0 base64enc_0.1-2 digest_0.6.8 DNAcopy_1.40.0 [5] MASS_7.3-40 matrixStats_0.14.0 PSCBS_0.44.0 R.cache_0.11.0 [9] R.huge_0.9.0 R.rsp_0.20.0 tools_3.1.3 -- -- 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/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
