Brlmm-P Cluster Centers

When I call genotypes with apt-probeset-genotype (Affymetrix Powertools, brlmm-p method), how do I get the cluster centers for each SNP?

Best regards, Stefanie

affymetrix snp

• 2,594 views • link

written 14.4 years ago by Steffi

0 answers

No answers yet.

More posts like this

PennCNV step1.1 error
written 3.1 years ago by jaredgichohi •

Hello, I am stuck at the initial step in the PennCNV CNV calling pipeline ie step 1.1 - generating genotype calls from raw CEL files. …
combine vcf files from differents genotypes
written 6.3 years ago by adrien.cv •

Dear, I perform the snp detection with Varscan on several genotypes. And now I tried to combine all vcf files in order to construct one …
How to run apt-geno-qc with call rate and treshold?
written 7.1 years ago by anamaria

Hello, I am trying to run apt-probeset-genotype from: https://media.affymetrix.com/support/developer/powertools/changelog/apt-probeset-genotype.html My data is: Affy500K They say there that: " For Mapping 500K data the recommended per-chip …
Affymetrix Power Tool: Wrong number of cells
written 8.2 years ago by ab555 •

I want to convert CEL format data using APT(Affymetrix Power Tool) as per its Affymetrix-PennCNV protocol but the APT command line is not letting me …
How to convert and annotate apt-probeset-genotype into PLINK format
written 10.5 years ago by Myosotis1979 •

Dear all, I called SNP genotypes of 100 Affy6 CEL files using apt-probeset-genotype from APT in order to perform a subsequent CNV analysis with PennCNV. …
APT: FATAL ERROR:Exception. msg: 'Missing required column: ' source file: 'PriorsReader.cpp:352'
written 11.3 years ago by thaisfernanda.godoy •

I've used APT to process the CEL files to generate the cross-marker normalized signal intensity data from Axiom Genome-wide Chicken Array (Affymetrix). I've used this …
Affymetrix HuGeneST_1.0 masking probes
written 11.9 years ago by lkmklsmn

Hi, in order to exclude any biased from socalled "SNP-in-probe" probes I want to mask certain probes when summarizing affymetrix probesets. I have a list …
Genotype, Baf And L2R For Axiom Exome
written 13.3 years ago by kuragari.ch •

<p>I am trying to extract certain information from Axiom and Axiom Exome arrays from Affymetrix. I have done the same for GenomeWildSNP 6 using oligo, …
Bwa: "Xt:A:U" And Mapq Of 0 At The Same Time
written 14.4 years ago by Steffi

<p>I map RNA-Seq Data with <a href='http://bio-bwa.sourceforge.net/'>BWA</a> to the genome. The output files from <a href='http://bio-bwa.sourceforge.net/'>BWA</a> in <a href='http://samtools.sourceforge.net/SAM1.pdf'>sam</a>-format contain reads that have on the …
Affymetrix Genotyper Console Output Using For Plink Run Of Homozygosity
written 14.8 years ago by Msa •

<p>Dear all, I have a .txt file (includes Chrom, Position, SnpId, Genotype) from Affymetrix Genotyper Console (Affymetrix SNP Array 6.0). Normally we put this into …