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• Tcga Illumina Methylation Combining 27K And 450K
  Hi everyone, There was a question on this long ago but no detailed answer was given to it, so I r...
• Human 450K methylation data: Tumor vs Normal vs Control
  Hello I intend to use Infinium/Illumina 450K human methylation array data in cancer studies. I n...
• Tcga Illumina Methylation Combining 27K And 450K
  I'd like to use a TCGA methylation dataset but some of the data is from the 27k Illumina platform...
• Averaging TCGA 450K Methylation Data within 500bp Windows Across all Samples
  Hi Everyone, I'm fairly new to bioinformatics and data processing, but up until now I was able t...
• How to normalized the different cancers of Level 3 TCGA data of DNA Methylation
  Hi, I just found different tumor-specific working groups may do the job differently. So although ...
• Batch correction for TCGA 450K data
  Hi, When working with Level 3 450K DNA methylation from TCGA, is there a batch correction and/or...
• How to normalize 450K data for cell type composition
  Hi, I've a bunch of 450K (Infinium HumanMethylation450 BeadChip) methylation data from leukemic ...
• Second normalization for TCGA data
  Hi, I'm now using the TCGA RNASeq data (Illumina Genome Analyzer) to do some screening for new in...
• How to analyze the 450K methylation data from UCSC Xena?
  Hi, there, I am working on the 450k methylation microarray data coming from the UCSC Xena. I pla...
• Require review/comments/suggestions on 450k analysis college project
  Hello everyone I am a beginner level bioinformatician planning to work on "Analysing and interpr...
• How can I look at nonsense mutations in a particular gene in TCGA data?
  I have been working with TCGA cancer data to examine expression (RNAseqV2) and methylation (Illum...
• Is there public (DNA methylation) data on circulating cell-free DNA - why not?
  In the near future, I will have to deal with circulating cell-free DNA in the context of finding ...
• Does RPKM value of TCGA data need to be normalized by reference gene?
  I'm new to NGS data analysis. Recently I am dealing with various types of TCGA cancer data from G...
• Your Thoughts On A "Standard" Pipeline To Process Illumina 450K Data
  I've recently started working with the Illumina 450K methylation platform. There are several soft...
• Is it possible to download cancer, normal, and matched tissue data from GDC? From same patient samples? How?
  I'm trying to download gene expression data from GDC. Ideally, I'd like to get normal, cancer, an...
• What package to use in bioconductor to draw heatmap like this
  Hi all, I'm new in this field, and I tried to cluster some TCGA cancer patients for further survi...
• Differential expression analysis for TCGA level 3 RNASeqV2 data?
  Hi! I am actually looking at TCGA level3 RNASeqV2 data. My goal is to look at the DEGs (tumor vs....
• Differential Expression Gene analysis using normalized data
  Hello. I'm working on RNA expression data from TCGA's pipeline. we have 'rsem_isoforms_normali...
• Is there an informative subset of 450k methylation probes?
  I'm working on an analysis which includes 450k methylation data. There are so many probes that an...
• GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
  TCGA has recently migrated to the Genomic Data Commons (GDC). Following this migration, many tool...
• Illumina EPIC methylation analysis with meffil
  I'm trying to run quality control on the new Illumina EPIC chip methylation data with the meffi...
• Are there any way to find DMR with the data in TCGA methylation level3?
  Hi dear all, after downloaded the illumina 450K methylation chip data from TCGA, I have identifi...
• Approaches for normalisation of Illumina 450k data with large global differences in methylation
  Hi, I was wondering if someone could comment on, or point me in the right direction of, consider...