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rsem
•
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0
votes
1
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302
views
tximport error with rsem files
rsem
tximport
updated 4 months ago by
ATpoint
★ 4.0k • written 4 months ago by
apolitics
• 0
1
vote
3
replies
856
views
Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue
Spati
RSEM
deno
DEseq2
updated 10 months ago by
lauryfriese932
• 0 • written 11 months ago by
shashank
• 0
1
vote
4
replies
1.3k
views
How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2 when DEGs
limma
edgeR
RSEM
updated 13 months ago by
Gordon Smyth
50k • written 13 months ago by
Yang Shi
▴ 10
1
vote
2
replies
622
views
Differential expression analysis based on EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2
DESeq2
limma
edgeR
RSEM
13 months ago
Yang Shi
▴ 10
2
votes
3
replies
1.2k
views
Error while reading rsem files in tximport
DESeq2
tximport
rsem
RNASeq
tximportData
16 months ago
mohammedtoufiq91
▴ 10
0
votes
3
replies
1.2k
views
Differential Expression Analysis on RNAseq - RSEM expected_count from UCSC RNA-Seq toil recompute
DESeq2
Toil
RSEM
17 months ago
Niveditha
▴ 20
4
votes
5
replies
2.1k
views
Which is the best type of data for correlation or survival analysis
TPM
RNASeq
RSEM
DESeq2
updated 20 months ago by
Michael Love
41k • written 20 months ago by
Yang Shi
▴ 10
5
votes
9
replies
1.8k
views
GSVA perfomed on RSEM Expected Count data
GSVA
RNA-Seq
RSEM
Expected_Count
21 months ago • updated 20 months ago
Yang Shi
▴ 10
5
votes
6
replies
1.7k
views
Removing the duplicated genes before limma::voom by using limma::avereps
RSEM
avereps
voom
limma
RNASeq
21 months ago
Yang Shi
▴ 10
2
votes
4
replies
1.3k
views
Doing normalization when using voom for DEG analysis?
limma
RSEM
voom
Normalization
21 months ago
Yang Shi
▴ 10
2
votes
8
replies
1.5k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM
tximport
scRNAseq
DESeq2
22 months ago • updated 21 months ago
Kelen
▴ 10
0
votes
0
replies
662
views
Proper normalization of batch effected corrected raw rsem rnaseq values for downstream unsupervised analyses
limma
RNASeq
rsem
Normalization
2.4 years ago
svlachavas
▴ 830
1
vote
4
replies
1.3k
views
TCGA data analysis
RSEM
3.0 years ago
lily
▴ 20
0
votes
1
reply
927
views
tximport error importing expected counts file from RSEM
RSEM
tximport
updated 3.3 years ago by
Michael Love
41k • written 3.3 years ago by
Muyu
• 0
0
votes
2
replies
1.4k
views
How well does "Trinity-Differential-Expression" work on normalized raw counts without RSEM abundance of estimation
Trinity
DifferentialExpression
RSEM
RNAseq
edgeR
3.4 years ago
harelarik
▴ 60
6
votes
6
replies
2.3k
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2
VST
rsem
tximport
3.4 years ago
svlachavas
▴ 830
0
votes
2
replies
1.5k
views
Use of RSEM counts in WGCNA
rsemmed
RSEM
WGCNA
3.4 years ago
harelarik
▴ 60
1
vote
4
replies
1.0k
views
tximport abundanceCol parameter not functioning for rsem data
tximport
rsem
transcript abundance
TPM
FPKM
updated 3.5 years ago by
Michael Love
41k • written 3.6 years ago by
m.metsger
• 0
6
votes
13
replies
5.0k
views
How to use RSEM value to find differentially expressed genes
RSEM
limma
edgeR
voom
normalization
updated 21 months ago by
Gordon Smyth
50k • written 3.6 years ago by
harelarik
▴ 60
0
votes
8
replies
1.8k
views
Importing RSEM with tximport
tximport
RSEM
import error
updated 3.6 years ago by
Michael Love
41k • written 3.6 years ago by
harelarik
▴ 60
2
votes
2
replies
948
views
RSEM for DESeq2 without abundance matrix
tximport
deseq2
rsem
updated 3.7 years ago by
Michael Love
41k • written 3.7 years ago by
le2336
▴ 20
1
vote
3
replies
827
views
RSEM and Tximport
RSEM
tximport
deseq2
updated 3.8 years ago by
James W. MacDonald
65k • written 3.8 years ago by
pthom010
• 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
0
votes
0
replies
780
views
Is the ballgownrsem function still supported?
ballgown
rsem
iranges
4.3 years ago
YH
• 0
0
votes
6
replies
2.5k
views
Large fold changes after deseq2 when one condition has two zeros and small number the other condition has two zeros and a large number
rnaseq
rsem
deseq2
5.6 years ago
loliveira
• 0
0
votes
0
replies
951
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown
rsem
iranges
5.8 years ago
kicheol.kim
• 0
1
vote
0
replies
2.0k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown
rsem
iranges
5.8 years ago
kicheol.kim
• 0
0
votes
1
reply
808
views
Using tximport on RSEM abundance date
rnaseq
rsem
tximport
updated 5.8 years ago by
Michael Love
41k • written 5.8 years ago by
raeganlynn123
• 0
1
vote
4
replies
1.2k
views
DE analysis of orthologs with varying sequence lengths using RSEM+tximport+DEseq2: normalization for sequence length?
deseq2
sequence length normalization
RSEM
tximport
differential expression
updated 5.8 years ago by
Michael Love
41k • written 5.8 years ago by
al-ash
▴ 50
0
votes
5
replies
1.3k
views
countsFromAbundance for gene-level RSEM import in tximport
tximport
rsem
updated 5.8 years ago by
Michael Love
41k • written 5.8 years ago by
celi0001
• 0
0
votes
0
replies
856
views
RSEM output in txtimport
RSEM
txtimport
5.9 years ago
gat2010
• 0
0
votes
8
replies
2.5k
views
Differences in gene length passed to DESeq2 by tximport reulted in different gene rankings
deseq2
tximport
rsem
saimon
updated 5.9 years ago by
Michael Love
41k • written 5.9 years ago by
LD
• 0
2
votes
18
replies
3.4k
views
Using tximport on rsem files produces error while trying to read in files
R
tximport
rnaseq
tpm
rsem
6.1 years ago
stephan.emmrich
▴ 10
2
votes
2
replies
1.0k
views
tximport failing at importing TPM instead of FPKM
tximport
rnaseq
rsem
updated 6.1 years ago by
rosabellascottgm
• 0 • written 6.1 years ago by
fresard.laure
• 0
3
votes
13
replies
2.4k
views
tximport's parameter for countsFromAbundance doesn't work
tximport
rsem
edger
6.2 years ago
tim.ivanov.92
• 0
0
votes
1
reply
1.2k
views
Data object format for deseq2
deseq2
R
RSEM
updated 6.3 years ago by
Michael Love
41k • written 6.3 years ago by
tim.ivanov.92
• 0
1
vote
2
replies
1.6k
views
RNA-seq read alignment best practices for low-input samples
limma
differential gene expression
rnaseq analysis
alignment
RSEM
updated 6.3 years ago by
Aaron Lun
★ 28k • written 6.3 years ago by
goldberg.jm
▴ 10
3
votes
4
replies
3.6k
views
Importing RSEM transcript-level data using tximport
tximport
rsem
updated 6.4 years ago by
Michael Love
41k • written 6.4 years ago by
Patrick Kimes
▴ 10
2
votes
11
replies
4.3k
views
Tximport with RSEM error
RSEM
updated 6.5 years ago by
k.vitting.seerup
▴ 120 • written 6.5 years ago by
hs.lansdell
▴ 20
2
votes
7
replies
2.0k
views
Obtaining transcript names in RSEM
tximport
rsem
updated 6.6 years ago by
Michael Love
41k • written 6.6 years ago by
deena
▴ 20
0
votes
2
replies
1.2k
views
Using RSEM reads for DESeq2
deseq2
rsem
updated 6.6 years ago by
Michael Love
41k • written 6.6 years ago by
deeptiptl74
▴ 10
3
votes
1
reply
1.5k
views
Filtering step in Differential analysis with RSEM values
rsem
differential gene expression
edger
updated 6.7 years ago by
Gordon Smyth
50k • written 6.7 years ago by
Biologist
▴ 110
0
votes
1
reply
1.8k
views
confusion with tximport options and resulting matrix
tximport
rnaseq
rsem
limma
voom
updated 6.7 years ago by
Gordon Smyth
50k • written 6.7 years ago by
arubio
• 0
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
6
votes
5
replies
3.8k
views
Clustering differential expression results from voomWithQualityWeights
RNA
limma
rsem
edgeR
updated 7.0 years ago by
Gordon Smyth
50k • written 7.0 years ago by
hrishi27n
▴ 20
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
1
reply
1.8k
views
RSEM output in DeSeq2
RSEM
deseq2
count matrix
updated 7.2 years ago by
Michael Love
41k • written 7.2 years ago by
kmeusemann
• 0
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
9
votes
5
replies
16k
views
Expected counts from RSEM in DESeq2
RSEM
deseq2
expected_counts
raw_counts
updated 2.8 years ago by
Michael Love
41k • written 7.3 years ago by
chudar.chudar
▴ 30
5
votes
9
replies
5.9k
views
Voom: need at least two non-NA values to interpolate
limma voom
voom
rsem
fpkm
7.6 years ago
komal.rathi
▴ 120
50 results • Page
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Comment: Error in champ.load(): The following specified files do not exist
by
Basti
▴ 760
The error stems from the Basename column, please see solution here : https://support.bioconductor.org/p/p132482/
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'…
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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