Showing : TCGA • reset
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One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools TCGA
19 months ago glaciya2018 • 0
9
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18
replies
4.7k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation qsea MEDIPS TCGA
updated 23 months ago by ▴ 280 • written 8.7 years ago by ▴ 20
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2
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1.3k
views
TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 2.1 years ago by ★ 1.1k • written 2.1 years ago by ▴ 200
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1
reply
981
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GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA GenomicDataCommons GDC
written 2.4 years ago by ▴ 510
1
vote
1
reply
951
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
1
vote
3
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1.9k
views
Can i perform DEseq2 from 2 different rse objects download from RECOUNT database
DESeq2 recount GTEx TCGA recount3
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by ▴ 20
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1
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1.2k
views
TCGA RNAseq Normalization
normalization RNASEQ Normalization TCGAutils TCGA
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
2
votes
9
replies
4.0k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
3.5 years ago • updated 3.4 years ago Peipei • 0
2
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2
replies
3.4k
views
Create TPM gene tables/dataframe from ReCount3
recount3 TCGA GTEx DESeq2
3.5 years ago David ▴ 20
3
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2
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3.1k
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Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC TCGA tcgabiolinks
updated 3.6 years ago by • 0 • written 7.0 years ago by ▴ 10
4
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5
replies
2.3k
views
GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks TCGA
updated 3.6 years ago by • 0 • written 5.2 years ago by ▴ 40
1
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1
reply
2.1k
views
recount3 - download bigwig files for TCGA data
recount3 recount TCGA
updated 3.7 years ago by ★ 1.1k • written 3.7 years ago by ▴ 10
0
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2
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1.4k
views
Removing paired samples for DESeq2 analysis
RNASeq DifferentialExpression DESeq2 tcga
3.8 years ago IamFrofro • 0
3
votes
2
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1.8k
views
How to obtain clinical data from TCGA via Bioconductor GenomicDataCommons
TCGA GenomicDataCommons
updated 4.0 years ago by ★ 3.4k • written 4.0 years ago by ▴ 10
5
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9
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4.5k
views
Error via running GDCquey from TCGAbiolinks package
TCGA Genome Data Common portal
updated 4.5 years ago by ▴ 10 • written 7.4 years ago by ▴ 10
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0
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1.2k
views
Determine whether RNAseq data from TCGA is paired or single-end?
TCGA TCGAbiolinks
4.6 years ago rebeliscu • 0
0
votes
1
reply
1.4k
views
Getting number of cases added by date to TCGA project with `GenomicDataCommons`
TCGA GenomicDataCommons
4.7 years ago Ezgi ▴ 60
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0
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1.4k
views
Job: PhD position in Developmental Neurobiology and Bioinformatics
rnaseq neurobiology tcga Job
5.1 years ago Laurent Gatto 1.6k
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0
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1.2k
views
Identify significantly different DNA methylation probes in tumor and normal samples GBM ELMER R package
ELMER TCGA GEO
5.2 years ago andrade4beatriz • 0
0
votes
5
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5.3k
views
Retrieve TCGA expression data for a single gene
TCGA TCGAbiolinks
updated 5.2 years ago by ▴ 260 • written 5.3 years ago by ▴ 40
4
votes
7
replies
5.9k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by • 0
0
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2
replies
2.1k
views
Recount2 Bigwigs for TCGA
R TCGA recount2 recount
updated 5.7 years ago by ★ 1.1k • written 5.7 years ago by • 0
4
votes
7
replies
1.9k
views
'NA' found under Gene Names in the list of top differentially expressed genes found using edgeR
edger differential expression TCGA Gene ID
updated 5.7 years ago by 68k • written 5.7 years ago by ▴ 60
0
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0
replies
1.1k
views
Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks GDC TCGA
6.0 years ago modarzi ▴ 10
0
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4
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1.9k
views
problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks TCGA GDC
6.0 years ago modarzi ▴ 10
2
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3
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1.1k
views
DESeq2 doesn't return the most drastically DEG
deseq2 tcga
6.1 years ago ndjayne • 0
2
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2
replies
3.8k
views
DESeq2: design = ~1 For Normalisation Only.
deseq2 limma normalization tcga rnaseq
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
1
vote
2
replies
1.8k
views
TCGAbiolinks : Bisulfite-seq data : Legacy archive
tcga bisulfite tcgabiolinks
updated 6.4 years ago by ▴ 260 • written 6.4 years ago by • 0
1
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1
reply
1.9k
views
TCGA isoform expression quantification file - how to reshape data
data.frame tcga reshape data
updated 6.5 years ago by ★ 13k • written 6.5 years ago by ▴ 160
1
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2
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1.9k
views
TCGA MAF (Mutations) data
TCGA MAF GDC snp mutations
updated 6.6 years ago by 21k • written 6.6 years ago by ▴ 160
0
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1
reply
1.7k
views
How to download the TCGA SKCM subtype information?
TCGA melanoma TCGA SKCM
6.6 years ago syrttgump ▴ 20
5
votes
4
replies
2.6k
views
Perform correlation analysis between miRNA and mRNA gene expression data on the same TCGA dataset based on the curatedTCGAData
curatedTCGAData MultiAssayExperiment multiomics TCGA
updated 6.7 years ago by ★ 1.1k • written 6.7 years ago by ▴ 840
0
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0
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1.5k
views
TCGAbiolinks specific mutation query
TCGAbiolinks TCGA Mutation GDCquery rnaseq
6.7 years ago Yonatan Amzaleg • 0
1
vote
3
replies
3.5k
views
Error via running GDCdownload() in TCGAbiolinks
TCGAbiolinks TCGA Download
updated 6.7 years ago by ▴ 260 • written 6.7 years ago by ▴ 10
4
votes
6
replies
4.6k
views
DESeq2 vst normalization: Do I have a heteroscedasticity problem and if so, what can I do about it?
deseq2 normalization rna-seq TCGA vst
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 70
1
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5
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2.4k
views
Issue with TCGAbiolinks package.
TCGA GDCprepare
6.8 years ago salvocomplicazioni1 • 0
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0
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1.2k
views
Reference for minimum number of probes commonly used for segmentation of microarray data
segmentation reference CNA TCGA
6.8 years ago jlarsen728 • 0
4
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2
replies
1.6k
views
GenomicDataCommons request timeouts when cases() %>% ... %>% results_all()
genomicdatacommons tcga gdc rest http
updated 6.9 years ago by 21k • written 6.9 years ago by ▴ 20
0
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0
replies
1.6k
views
Tumor subtype classification when genes of gene set are missing from samples - GSVA approach
GSVA geneset RNASeq TCGA subtypes
6.9 years ago Pietro ▴ 40
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0
replies
1.3k
views
GDC RNA seq files (replicates?)
gdc data TCGA gdcdownload
6.9 years ago coyoung ▴ 10
2
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4
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1.9k
views
edgeR. Known cancer genes are not differentially expressed?
edger tcga
updated 7.0 years ago by ★ 29k • written 7.0 years ago by ▴ 30
0
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1
reply
1.5k
views
RNAseq gene expression analysis in Personalized genomics
TCGA deseq2 edger limma
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
2
votes
3
replies
2.2k
views
Problem for finding "Locus Link ID" from Annotation file
wgcna package TCGA LocusLinkID genecode ensembl
updated 7.1 years ago by 68k • written 7.1 years ago by ▴ 10
8
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12
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8.3k
views
MultiAssayExperiment: Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
multiassayexperiment wide format TCGA
updated 7.2 years ago by 700 • written 7.2 years ago by ▴ 160
8
votes
8
replies
8.8k
views
Voom transformation from counts and normalization to negative values
rnaseq voom limma tcga statistics
updated 7.2 years ago by ★ 7.9k • written 7.2 years ago by ▴ 60
1
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2
replies
1.7k
views
how to output and get the normalization gene expression data (similar to the FPKM gene expression data) from reads count data by DESeq2 and edgeR?
deseq2 edger fpkm counts TCGA
updated 7.2 years ago by 53k • written 7.2 years ago by • 0
3
votes
4
replies
3.4k
views
TCGA biolinks - Samples with multiple profiles
tcgabiolinks tcga genomicdatacommon
7.3 years ago gamma.jian ▴ 10
0
votes
5
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3.0k
views
DNA methylation analysis without raw data IDAT files
r illimina 450k methylation minfi champ tcga
updated 7.3 years ago by ▴ 290 • written 7.3 years ago by ▴ 60
4
votes
2
replies
3.2k
views
Where to download expected counts instead of normalized RSEM for TCGA LUAD?
limma tcga
updated 7.3 years ago by ★ 13k • written 7.3 years ago by ▴ 60
0
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2
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3.2k
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Error: vector memory exhausted (limit reached?)
tcgabiolinks tcga cnv mac os x gaia
updated 7.3 years ago by ▴ 20 • written 7.3 years ago by ▴ 30
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Comment: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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