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TCGA
•
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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
13
votes
20
replies
13k
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
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
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
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
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
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
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
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
1
vote
3
replies
4.1k
views
R Text progress bar error
TCGA
8.3 years ago
devyani66
• 0
4
votes
7
replies
3.9k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2
tximport
tcga
rsem
firebrowse
updated 3.9 years ago by
Kevin Blighe
★ 3.9k • written 3.9 years ago by
J. Smith
• 0
2
votes
0
replies
3.8k
views
Tutorial:
BoF Bioc2017: Analyzing publicly available cancer genomics data from GTEx and TCGA with Bioconductor
public data
TCGA
GTEx
Tutorial
6.7 years ago
shepherl
3.8k
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
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
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
4
votes
6
replies
3.5k
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 5.2 years ago by
Michael Love
41k • written 5.2 years ago by
Marc Saric
▴ 70
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
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
0
votes
2
replies
3.3k
views
Pipeline for analyzing CNV (SNP array) level 3 from TCGA
SNP
CNV
TCGA
9.0 years ago
NS
▴ 60
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
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
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
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
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
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
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
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
0
replies
2.5k
views
How to normalize-transform rsem.genes.results of TCGA RNA-seq v2?
tcga
rnaseq
rsem
R
normalization
7.1 years ago
panagiotis.mokos
▴ 40
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
0
votes
0
replies
2.4k
views
TCGA RSEM normalized RNAseqV2 counts
normalization
cancer
tcga
9.0 years ago
ezz
• 0
3
votes
4
replies
2.3k
views
TCGA biolinks - Samples with multiple profiles
tcgabiolinks
tcga
genomicdatacommon
5.6 years ago
franceschini.gianmarco
• 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
2
votes
2
replies
2.2k
views
DESeq2: design = ~1 For Normalisation Only.
deseq2
limma
normalization
tcga
rnaseq
updated 4.5 years ago by
Michael Love
41k • written 4.5 years ago by
Alex Greenshields-Watson
• 0
2
votes
9
replies
2.2k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA
r
RNASeqData
voom
limma
22 months ago
Peipei
• 0
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
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
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
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
1
vote
3
replies
2.0k
views
Error via running GDCdownload() in TCGAbiolinks
TCGAbiolinks
TCGA
Download
updated 5.1 years ago by
Tiago Chedraoui Silva
▴ 260 • written 5.1 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
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
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
1.9k
views
Create TPM gene tables/dataframe from ReCount3
recount3
TCGA
GTEx
DESeq2
22 months ago
David
▴ 20
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
5
votes
4
replies
1.8k
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 5.0 years ago by
Levi Waldron
★ 1.1k • written 5.0 years ago by
svlachavas
▴ 830
1
vote
0
replies
1.8k
views
Problem about module preservation statistics in WGCNA software
rnaseq
tcga
wgcna
7.0 years ago • updated 6.9 years ago
panagiotis.mokos
▴ 40
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
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
0
votes
4
replies
1.6k
views
TCGABiolinks not available for R3.3.0
TCGA
tcgabiolinks
R
updated 7.8 years ago by
Martin Morgan
25k • written 7.8 years ago by
j.ritchie
• 0
50 results • Page
1 of 1
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Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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