Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
rsem
•
reset
1
vote
3
replies
572
views
Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue
Spati
RSEM
deno
DEseq2
updated 5 months ago by
lauryfriese932
• 0 • written 6 months ago by
shashank
• 0
1
vote
4
replies
804
views
How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2 when DEGs
limma
edgeR
RSEM
updated 8 months ago by
Gordon Smyth
48k • written 8 months ago by
Yang Shi
▴ 10
1
vote
2
replies
420
views
Differential expression analysis based on EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2
DESeq2
limma
edgeR
RSEM
8 months ago
Yang Shi
▴ 10
2
votes
3
replies
902
views
Error while reading rsem files in tximport
DESeq2
tximport
rsem
RNASeq
tximportData
12 months ago
mohammedtoufiq91
▴ 10
0
votes
3
replies
834
views
Differential Expression Analysis on RNAseq - RSEM expected_count from UCSC RNA-Seq toil recompute
DESeq2
Toil
RSEM
13 months ago
Niveditha
▴ 20
4
votes
5
replies
1.7k
views
Which is the best type of data for correlation or survival analysis
TPM
RNASeq
RSEM
DESeq2
updated 15 months ago by
Michael Love
41k • written 16 months ago by
Yang Shi
▴ 10
5
votes
9
replies
1.5k
views
GSVA perfomed on RSEM Expected Count data
GSVA
RNA-Seq
RSEM
Expected_Count
16 months ago
Yang Shi
▴ 10
5
votes
6
replies
1.3k
views
Removing the duplicated genes before limma::voom by using limma::avereps
RSEM
avereps
voom
limma
RNASeq
16 months ago
Yang Shi
▴ 10
2
votes
4
replies
954
views
Doing normalization when using voom for DEG analysis?
limma
RSEM
voom
Normalization
16 months ago
Yang Shi
▴ 10
2
votes
8
replies
1.2k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM
tximport
scRNAseq
DESeq2
17 months ago
Kelen
▴ 10
0
votes
0
replies
546
views
Proper normalization of batch effected corrected raw rsem rnaseq values for downstream unsupervised analyses
limma
RNASeq
rsem
Normalization
2.1 years ago
svlachavas
▴ 820
1
vote
4
replies
1.2k
views
TCGA data analysis
RSEM
2.7 years ago • updated 2.6 years ago
lily
▴ 20
0
votes
1
reply
796
views
tximport error importing expected counts file from RSEM
RSEM
tximport
updated 2.9 years ago by
Michael Love
41k • written 2.9 years ago by
Muyu
• 0
0
votes
2
replies
1.2k
views
How well does "Trinity-Differential-Expression" work on normalized raw counts without RSEM abundance of estimation
Trinity
DifferentialExpression
RSEM
RNAseq
edgeR
3.0 years ago
harelarik
▴ 60
6
votes
6
replies
2.1k
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2
VST
rsem
tximport
3.0 years ago
svlachavas
▴ 820
0
votes
2
replies
1.3k
views
Use of RSEM counts in WGCNA
rsemmed
RSEM
WGCNA
3.0 years ago
harelarik
▴ 60
1
vote
4
replies
876
views
tximport abundanceCol parameter not functioning for rsem data
tximport
rsem
transcript abundance
TPM
FPKM
updated 3.1 years ago by
Michael Love
41k • written 3.2 years ago by
m.metsger
• 0
6
votes
13
replies
4.4k
views
How to use RSEM value to find differentially expressed genes
RSEM
limma
edgeR
voom
normalization
updated 16 months ago by
Gordon Smyth
48k • written 3.3 years ago by
harelarik
▴ 60
0
votes
8
replies
1.5k
views
Importing RSEM with tximport
tximport
RSEM
import error
updated 3.3 years ago by
Michael Love
41k • written 3.3 years ago by
harelarik
▴ 60
2
votes
2
replies
829
views
RSEM for DESeq2 without abundance matrix
tximport
deseq2
rsem
updated 3.3 years ago by
Michael Love
41k • written 3.3 years ago by
le2336
▴ 20
1
vote
3
replies
726
views
RSEM and Tximport
RSEM
tximport
deseq2
updated 3.5 years ago by
James W. MacDonald
64k • written 3.5 years ago by
pthom010
• 0
4
votes
7
replies
3.4k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2
tximport
tcga
rsem
firebrowse
updated 3.5 years ago by
Kevin Blighe
3.9k • written 3.5 years ago by
J. Smith
• 0
0
votes
0
replies
680
views
Is the ballgownrsem function still supported?
ballgown
rsem
iranges
4.0 years ago • updated 3.9 years ago
YH
• 0
0
votes
6
replies
2.3k
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
5.2 years ago
loliveira
• 0
0
votes
0
replies
844
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown
rsem
iranges
5.4 years ago
kicheol.kim
• 0
1
vote
0
replies
1.9k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown
rsem
iranges
5.4 years ago
kicheol.kim
• 0
0
votes
1
reply
685
views
Using tximport on RSEM abundance date
rnaseq
rsem
tximport
updated 5.4 years ago by
Michael Love
41k • written 5.4 years ago by
raeganlynn123
• 0
1
vote
4
replies
1.1k
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 5.4 years ago by
Michael Love
41k • written 5.4 years ago by
al-ash
▴ 50
0
votes
5
replies
1.1k
views
countsFromAbundance for gene-level RSEM import in tximport
tximport
rsem
updated 5.5 years ago by
Michael Love
41k • written 5.5 years ago by
celi0001
• 0
0
votes
0
replies
770
views
RSEM output in txtimport
RSEM
txtimport
5.5 years ago
gat2010
• 0
0
votes
8
replies
2.3k
views
Differences in gene length passed to DESeq2 by tximport reulted in different gene rankings
deseq2
tximport
rsem
saimon
updated 5.5 years ago by
Michael Love
41k • written 5.5 years ago by
LD
• 0
2
votes
18
replies
3.1k
views
Using tximport on rsem files produces error while trying to read in files
R
tximport
rnaseq
tpm
rsem
5.7 years ago
stephan.emmrich
▴ 10
2
votes
2
replies
924
views
tximport failing at importing TPM instead of FPKM
tximport
rnaseq
rsem
updated 5.8 years ago by
rosabellascottgm
• 0 • written 5.8 years ago by
fresard.laure
• 0
3
votes
13
replies
2.0k
views
tximport's parameter for countsFromAbundance doesn't work
tximport
rsem
edger
5.8 years ago
tim.ivanov.92
• 0
0
votes
1
reply
1.1k
views
Data object format for deseq2
deseq2
R
RSEM
updated 5.9 years ago by
Michael Love
41k • written 5.9 years ago by
tim.ivanov.92
• 0
1
vote
2
replies
1.4k
views
RNA-seq read alignment best practices for low-input samples
limma
differential gene expression
rnaseq analysis
alignment
RSEM
updated 6.0 years ago by
Aaron Lun
★ 28k • written 6.0 years ago by
goldberg.jm
▴ 10
3
votes
4
replies
3.2k
views
Importing RSEM transcript-level data using tximport
tximport
rsem
updated 6.0 years ago by
Michael Love
41k • written 6.0 years ago by
Patrick Kimes
▴ 10
2
votes
11
replies
3.9k
views
Tximport with RSEM error
RSEM
updated 6.1 years ago by
k.vitting.seerup
▴ 120 • written 6.1 years ago by
hs.lansdell
▴ 20
2
votes
7
replies
1.7k
views
Obtaining transcript names in RSEM
tximport
rsem
updated 6.2 years ago by
Michael Love
41k • written 6.2 years ago by
deena
▴ 20
0
votes
2
replies
1.1k
views
Using RSEM reads for DESeq2
deseq2
rsem
updated 6.3 years ago by
Michael Love
41k • written 6.3 years ago by
deeptiptl74
▴ 10
3
votes
1
reply
1.4k
views
Filtering step in Differential analysis with RSEM values
rsem
differential gene expression
edger
updated 6.3 years ago by
Gordon Smyth
48k • written 6.3 years ago by
Biologist
▴ 110
0
votes
1
reply
1.6k
views
confusion with tximport options and resulting matrix
tximport
rnaseq
rsem
limma
voom
updated 6.4 years ago by
Gordon Smyth
48k • written 6.4 years ago by
arubio
• 0
1
vote
3
replies
2.4k
views
Differential analysis with RSEM normalized counts using limma without voom
limma
differential gene expression
tcga
rsem
updated 6.4 years ago by
James W. MacDonald
64k • written 6.4 years ago by
Biologist
▴ 110
6
votes
5
replies
3.5k
views
Clustering differential expression results from voomWithQualityWeights
RNA
limma
rsem
edgeR
updated 6.6 years ago by
Gordon Smyth
48k • written 6.6 years ago by
hrishi27n
▴ 20
0
votes
0
replies
2.4k
views
How to normalize-transform rsem.genes.results of TCGA RNA-seq v2?
tcga
rnaseq
rsem
R
normalization
6.7 years ago
panagiotis.mokos
▴ 40
0
votes
1
reply
1.7k
views
RSEM output in DeSeq2
RSEM
deseq2
count matrix
updated 6.8 years ago by
Michael Love
41k • written 6.8 years ago by
kmeusemann
• 0
25
votes
37
replies
10k
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 6.9 years ago by
Gordon Smyth
48k • written 6.9 years ago by
svlachavas
▴ 820
9
votes
5
replies
15k
views
Expected counts from RSEM in DESeq2
RSEM
deseq2
expected_counts
raw_counts
updated 2.4 years ago by
Michael Love
41k • written 6.9 years ago by
chudar.chudar
▴ 20
5
votes
9
replies
5.7k
views
Voom: need at least two non-NA values to interpolate
limma voom
voom
rsem
fpkm
7.2 years ago
komal.rathi
▴ 110
0
votes
8
replies
1.8k
views
Using Scran with RSEM/DEseq
scran
normalization
deseq2
rsem
edger
7.3 years ago
a.guerra
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: GOslim missing GO term
by
amanda
• 0
Thank you for the advice and many thanks! It is WGCNA analysis. I will try your method today and see if there are some consistencies.
Comment: GOslim missing GO term
by
James W. MacDonald
64k
Is this a WGCNA analysis (multiple co-expression clusters sounds like WGCNA)? If so, none of that is inferential or easily interpreted. It …
Comment: GOslim missing GO term
by
amanda
• 0
For each group, I generated multiple co-expression clusters, and within each cluster, cluster PC1 was correlated with PC1 of multiple clini…
Comment: GOslim missing GO term
by
James W. MacDonald
64k
What do you mean by 'enriched with ... GO terms from their correlations with clinical traits'? Are you doing a GO hypergeometric or somethi…
Comment: GOslim missing GO term
by
amanda
• 0
I have multiple groups to compare with, and each enriched with hundreds of GO terms from their correlations with clinical traits (top1 pval…
Votes
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: limma::voom vs edgeR::voomLmFit - when to use?
Answer: limma::voom vs edgeR::voomLmFit - when to use?
Awards
• All
Scholar
to
James W. MacDonald
64k
Scholar
to
Assa Yeroslaviz
★ 1.5k
Popular Question
to
Gordon Smyth
48k
Popular Question
to
Endre Sebestyén
▴ 70
Popular Question
to
ramonfallon
▴ 20
Locations
• All
Austria,
38 minutes ago
Thailand,
1 hour ago
United States,
1 hour ago
WEHI, Melbourne, Australia,
2 hours ago
United Kingdom,
2 hours ago
Traffic: 454 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6