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• Pca Plot For Microarray Data
  Hi, I have microarray (Agilent) data with me. I have done most of the analysis stuff which were ...
• How to use CNV kit?
  From TCGA microarray CNV data, which is level_3 data with segment means, if I use the CNV package...
• How to make a PCA plot to check similar samples between two cohorts?
  I have 20 samples with gene intensities from Microarrays and same 20 samples with counts from RNA...
• How do I explain to my non-bioinformatician labmates how to interpret principal components?
  I'm training to become a bioinformatician in a lab where everyone else is a traditional wet lab s...
• how to plot PCA for microarray normalized data
  Hi, I have RMA normalised file from microarray gene chip I have 4 groups A,B,C,D(4 sample in gro...
• pca analysis for differential gene expression data of microarray samples of similar condition
  i have the genes in rows and the sample names in the columns and number samples are 76 and numbe...
• 3D PCA Plot from RNA-Seq data
  I want to make 3d PCA plot with 2 components from RNA-Seq data. 3D Plot Refer following link fo...
• DESeq PCA plot and edgeR MDS plot
  Both of the tools use different kind of data transformation for doing PCA plots. However, in the...
• Is there a way to plot the data of the microarray color-coded using some data such as GO term?
  I am trying to plot microarray data on 2D plane by PCA and t-SNE now. So, I'd like to colorize ...
• Draw centromere on chromosome scatter plot
  Hello, I run CNVkit with my somatic data. I draw scatter plot, of the chromosomes. Sometimes the...
• Detect CNVs in single sample using cn.MOPS
  Hi all, Using cn.MOPS for CNV detection and it requires optimally 6 samples (6 BAM files) to eff...
• CNV/LOH from RNAseq
  Could I use RNAseq data from healthy and tumour samples to determine chromosome abnormalities?
• EXOMECNV segmentation algorithm
  I am calling the CNVs from canine data using ExomeCNV. The organism has 38 pairs of chromosome an...
• Meaning of TCGA CNV data
  I need to do some statistical calculation on CNV data that is publicly available in TCGA website....
• What values should I use for principle component analysis of microarray data?
  I have been doing a bit of reading about Principle Component Analysis (PCA) and have been using R...
• Retrieve Information From Ucsc Genome Browser ?
  For each chromosome of my sample I draw a cnv plot but I want to retrieve the CNV region (CNV val...
• PCA plot for methylated fragments
  Hi I would like to create a PCA plot on samples to see how 15 samples in my data group based on ...
• R plot.DNAcopy with x-axis showing chromosome instead of chromosome coordinate
  I was trying to plot CNV with plot.DNAcopy (a function in DNAcopy library). The input is standard...