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TCGA
•
reset
13
votes
20
replies
14k
views
Can I feed TCGA normalized count data to EdgeR for differential gene expression analysis
EdgeR
TCGA
normalized count
updated 9.1 years ago by
alakatos
▴ 130 • written 9.1 years ago by
ycding
▴ 10
9
votes
9
replies
5.2k
views
Voom on TCGA data shifts count distributions towards negative values
voom
TCGA
RNAseq
9.4 years ago
paola.ostano
▴ 10
25
votes
37
replies
11k
views
Possible ways of performing differential gene expression and analysis of RNA-Seq data from normalized counts of RSEM software
rnaseq
RSEM
TCGA
edgeR
normalization
updated 7.3 years ago by
Gordon Smyth
50k • written 7.3 years ago by
svlachavas
▴ 830
7
votes
18
replies
2.9k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation
qsea
MEDIPS
TCGA
updated 3 months ago by
Matthias Lienhard
▴ 240 • written 7.0 years ago by
justinburgener
▴ 20
1
vote
3
replies
4.1k
views
R Text progress bar error
TCGA
8.3 years ago
devyani66
• 0
1
vote
4
replies
3.4k
views
Different clustering results of DESeq2 counts and rlog
tcga
nomalization
rnaseq
deseq2
8.9 years ago
ezz
• 0
2
votes
5
replies
1.5k
views
GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks
TCGA
updated 24 months ago by
biologsr
• 0 • written 3.6 years ago by
aush
▴ 40
3
votes
2
replies
2.1k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC
TCGA
tcgabiolinks
updated 2.0 years ago by
cute scientist
• 0 • written 5.4 years ago by
Antonio Ahn
▴ 10
6
votes
14
replies
2.9k
views
Difficulty in finding DEG using TCGA data from FireBrowse
TCGA
FireBrowse
limma
DEG
updated 6.0 years ago by
svlachavas
▴ 830 • written 6.0 years ago by
lawarde.ankita1
▴ 30
3
votes
2
replies
1.0k
views
Can i add an experiment to an existing MultiAssayExperiment?
mutiassayexperiment
tcga
tcia
6.1 years ago
mario.zanfardino
▴ 160
5
votes
6
replies
6.3k
views
proper transformation for differential expression in normalized log expression data
tcga
rnaseq
deseq2
vsn
edger
updated 9.3 years ago by
Gordon Smyth
50k • written 9.3 years ago by
rachel.melamed
• 0
1
vote
7
replies
2.0k
views
Cannot retrieve projects from TCGA using getGDCprojects function
tcgabiolinks
TCGA
software error
6.4 years ago
jacorvar
▴ 40
0
votes
5
replies
2.1k
views
DNA methylation analysis without raw data IDAT files
r
illimina 450k methylation
minfi
champ
tcga
updated 5.7 years ago by
Yuan Tian
▴ 270 • written 5.7 years ago by
Beginner
▴ 60
0
votes
5
replies
2.7k
views
Retrieve TCGA expression data for a single gene
TCGA
TCGAbiolinks
updated 3.6 years ago by
Tiago Chedraoui Silva
▴ 260 • written 3.6 years ago by
aush
▴ 40
0
votes
2
replies
3.4k
views
Going crazy with normalizing TCGA raw rsem gene count
cancer
tcga
normalization
rnaseq
differential gene expression
updated 6.1 years ago by
Dimitris Vavoulis
• 0 • written 9.0 years ago by
ezz
• 0
0
votes
2
replies
1.1k
views
Recount2 TCGA metadata missing sample, run and experiment columns
recount
metadata
tcga
updated 6.1 years ago by
rosabellascottgm
• 0 • written 6.1 years ago by
Mariela Cortés-López
• 0
0
votes
2
replies
21k
views
Determining gene expression levels with DESeq2 in a design with no condition
deseq2
tcga
6.4 years ago
robles.daniela
• 0
2
votes
3
replies
1.4k
views
Problem for finding "Locus Link ID" from Annotation file
wgcna package
TCGA
LocusLinkID
genecode
ensembl
updated 5.5 years ago by
James W. MacDonald
65k • written 5.5 years ago by
modarzi
▴ 10
0
votes
3
replies
1.5k
views
Mapping of two different regions to one gene symbol
TCGA
CNV
updated 8.9 years ago by
Marc Carlson
★ 7.2k • written 8.9 years ago by
NS
▴ 60
0
votes
1
reply
1.1k
views
RNAseq gene expression analysis in Personalized genomics
TCGA
deseq2
edger
limma
updated 5.5 years ago by
Michael Love
41k • written 5.5 years ago by
bioc.vkas
• 0
0
votes
2
replies
3.7k
views
Extract gene expression values from GDCprepare object
tcgabiolinks
tcga
tcgadownload
gdcprepare
gdc
updated 7.1 years ago by
Tiago Chedraoui Silva
▴ 260 • written 7.2 years ago by
enigmargs
• 0
1
vote
2
replies
1.2k
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 5.6 years ago by
Gordon Smyth
50k • written 5.6 years ago by
ZihaoXing
• 0
8
votes
12
replies
6.1k
views
MultiAssayExperiment: Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
multiassayexperiment
wide format
TCGA
updated 5.6 years ago by
Marcel Ramos
690 • written 5.6 years ago by
mario.zanfardino
▴ 160
8
votes
8
replies
6.7k
views
Voom transformation from counts and normalization to negative values
rnaseq
voom
limma
tcga
statistics
updated 5.6 years ago by
Ryan C. Thompson
★ 7.9k • written 5.6 years ago by
Beginner
▴ 60
2
votes
6
replies
2.0k
views
Using TCGAbiolinks for exon and oligonucleotide level microarray
tcga
tcgabiolinks
microarray
exons
oligonucleotide
updated 7.9 years ago by
Tiago C. Silva
▴ 270 • written 7.9 years ago by
Fernando
• 0
6
votes
7
replies
1.7k
views
Download TCGA dataset like a S4 object
dataset
tcga
updated 5.7 years ago by
mario.zanfardino
▴ 160 • written 5.7 years ago by
Giuseppe
▴ 20
0
votes
2
replies
2.5k
views
Error: vector memory exhausted (limit reached?)
tcgabiolinks
tcga
cnv
mac os x
gaia
updated 5.7 years ago by
rreck
▴ 20 • written 5.7 years ago by
rina
▴ 30
3
votes
12
replies
3.8k
views
Problem about use of TCGA rna-seq rsem gene results for regularized cox regression modeling
tcga
rnaseq
glmnet
voom
deseq2
7.1 years ago
panagiotis.mokos
▴ 40
0
votes
1
reply
1.2k
views
LuminalA Breast cancer subtype samples from GEO GSE62944
tcga
cancer
BreastCancer
gse62944
luminalA
updated 8.0 years ago by
phil.chapman
▴ 150 • written 8.0 years ago by
hamda.binte.ajmal
• 0
4
votes
3
replies
2.9k
views
DESeq2 - design for TCGA level 3 data
deseq2
tcga
experimental design
multiple factor design
updated 8.9 years ago by
Michael Love
41k • written 8.9 years ago by
anand m t
▴ 40
0
votes
2
replies
1.3k
views
Differential gene expression analysis for GSE62944
R
limma
cancer
tcga
bioconductor
updated 8.1 years ago by
Valerie Obenchain
★ 6.8k • written 8.1 years ago by
hamda.binte.ajmal
• 0
5
votes
9
replies
3.2k
views
Error via running GDCquey from TCGAbiolinks package
TCGA
Genome Data Common portal
updated 2.9 years ago by
H. Z. Amini
▴ 10 • written 5.8 years ago by
modarzi
▴ 10
4
votes
2
replies
2.0k
views
Where to download expected counts instead of normalized RSEM for TCGA LUAD?
limma
tcga
updated 5.7 years ago by
Steve Lianoglou
★ 13k • written 5.7 years ago by
Ahdee
▴ 50
0
votes
1
reply
1.1k
views
Error downloading the package
tcgabiolinks
TCGA
DOWNLOAD
updated 6.6 years ago by
James W. MacDonald
65k • written 6.6 years ago by
sup230
▴ 30
0
votes
3
replies
1.4k
views
TCGAvisualize_EAbarplot Function Issue
tcga
updated 6.5 years ago by
eshelden
▴ 40 • written 8.1 years ago by
pgreylin
• 0
1
vote
4
replies
2.3k
views
Error on creation of DESEq2 object
deseq2
tcga
updated 7.4 years ago by
Michael Love
41k • written 7.4 years ago by
jarod_v6@libero.it
▴ 40
1
vote
2
replies
4.7k
views
Differential Analysis for gene expression from TCGA (Level 3)
limma
microarray
tcga
updated 9.0 years ago by
Steve Lianoglou
★ 13k • written 9.0 years ago by
hudacdif
• 0
1
vote
2
replies
3.0k
views
DESeq2/edgeR DEG analysis data input from TCGA and correation analysis
edgeR
TCGA
updated 6.6 years ago by
Aaron Lun
★ 28k • written 6.6 years ago by
JackieMe
• 0
17
votes
8
replies
3.1k
views
How to check the read length for all the TCGA data samples in GDC?
gdc
tcga
wes
gdc data
updated 6.0 years ago by
Sean Davis
21k • written 6.0 years ago by
Biologist
▴ 110
0
votes
4
replies
2.0k
views
DEseq2: any problem with unbalanced number of sample in normal/tumor study?
deseq2
rnaseq
tcga
updated 6.5 years ago by
Michael Love
41k • written 6.5 years ago by
bharata1803
▴ 60
2
votes
2
replies
2.2k
views
TCGAbiolinks Download ERROR
TCGA
tcgabiolinks
download
error
updated 6.5 years ago by
eshelden
▴ 40 • written 6.5 years ago by
Talip Zengin
▴ 10
2
votes
1
reply
2.1k
views
Error in TCGAquery of TCGAbiolinks Package
software error
bioconductor
tcgabiolinks
tcga
r
updated 5.9 years ago by
Benjamin Ostendorf
▴ 90 • written 5.9 years ago by
Beginner
▴ 60
1
vote
3
replies
2.6k
views
Differential analysis with RSEM normalized counts using limma without voom
limma
differential gene expression
tcga
rsem
updated 6.8 years ago by
James W. MacDonald
65k • written 6.8 years ago by
Biologist
▴ 110
0
votes
3
replies
1.5k
views
Analysing TCGA Level 3 Copy Number Data Location of markers in the genome
TCGA
Cancer
dnacopy
segmentation
updated 6.8 years ago by
markus.riester
▴ 130 • written 6.8 years ago by
Luisa672
• 0
1
vote
2
replies
1.6k
views
DESeq2 - Design for TCGA unpaired RNAseq data
DESeq2
design
TCGA
unpaired
RNAseq
updated 6.3 years ago by
Michael Love
41k • written 6.3 years ago by
Talip Zengin
▴ 10
2
votes
1
reply
4.7k
views
Using DESeq2 to analyse TCGA data
deseq2
tcga
tcgabiolinks
gene expression
differential expression
updated 6.2 years ago by
Michael Love
41k • written 6.2 years ago by
victor.ramos.usp
• 0
0
votes
2
replies
3.5k
views
Error using TCGAbiolinks "Error in fix.by(by.y, y) : 'by' must specify a uniquely valid column"
TCGA
tcgabiolinks
Error
6.8 years ago
f.geist
▴ 20
2
votes
2
replies
1.4k
views
Number of IRanges elements in TCGA HiSeqV2 dataset
r
tcga
recount
iranges
updated 6.9 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.9 years ago by
biomiha
▴ 20
0
votes
1
reply
1.5k
views
mutational signatures problems
bsgenome
readvcf
tcga
annotation
somaticsignatures
updated 8.1 years ago by
Julian Gehring
★ 1.3k • written 8.1 years ago by
jolligoodfellow
• 0
8
votes
5
replies
1.9k
views
Querying specific TCGA datasets through the MultiAssayExperiment R package
MultiAssayExperiment
curatedCRCdata
multiomics
TCGA
updated 5.8 years ago by
Marcel Ramos
690 • written 5.8 years ago by
svlachavas
▴ 830
50 results • Page
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