Showing : RSEM • reset
1
vote
2
replies
154
views
Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue Spati RSEM deno DEseq2
23 days ago • updated 22 days ago shashank • 0
1
vote
4
replies
245
views
How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2 when DEGs
limma edgeR RSEM
updated 10 weeks ago by 47k • written 10 weeks ago by ▴ 10
1
vote
2
replies
167
views
Differential expression analysis based on EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2
DESeq2 limma edgeR RSEM
11 weeks ago Yang Shi ▴ 10
2
votes
3
replies
513
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
6 months ago mohammedtoufiq91 ▴ 10
0
votes
3
replies
348
views
Differential Expression Analysis on RNAseq - RSEM expected_count from UCSC RNA-Seq toil recompute
DESeq2 Toil RSEM
7 months ago Niveditha ▴ 20
4
votes
5
replies
1.1k
views
Which is the best type of data for correlation or survival analysis
TPM RNASeq RSEM DESeq2
updated 9 months ago by 40k • written 10 months ago by ▴ 10
5
votes
9
replies
922
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
10 months ago Yang Shi ▴ 10
5
votes
6
replies
761
views
Removing the duplicated genes before limma::voom by using limma::avereps
RSEM avereps voom limma RNASeq
10 months ago Yang Shi ▴ 10
2
votes
4
replies
516
views
Doing normalization when using voom for DEG analysis?
limma RSEM voom Normalization
10 months ago Yang Shi ▴ 10
2
votes
8
replies
846
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
11 months ago Kelen ▴ 10
0
votes
0
replies
387
views
Proper normalization of batch effected corrected raw rsem rnaseq values for downstream unsupervised analyses
limma RNASeq rsem Normalization
18 months ago svlachavas ▴ 810
1
vote
4
replies
945
views
TCGA data analysis
RSEM
2.2 years ago • updated 2.1 years ago lily ▴ 20
0
votes
1
reply
630
views
tximport error importing expected counts file from RSEM
RSEM tximport
updated 2.4 years ago by 40k • written 2.4 years ago by • 0
0
votes
2
replies
1.0k
views
How well does "Trinity-Differential-Expression" work on normalized raw counts without RSEM abundance of estimation
Trinity DifferentialExpression RSEM RNAseq edgeR
2.5 years ago harelarik ▴ 60
6
votes
6
replies
1.8k
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2 VST rsem tximport
2.5 years ago svlachavas ▴ 810
0
votes
2
replies
1.1k
views
Use of RSEM counts in WGCNA
rsemmed RSEM WGCNA
2.5 years ago harelarik ▴ 60
1
vote
4
replies
706
views
tximport abundanceCol parameter not functioning for rsem data
tximport rsem transcript abundance TPM FPKM
updated 2.6 years ago by 40k • written 2.7 years ago by • 0
6
votes
13
replies
3.4k
views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
updated 10 months ago by 47k • written 2.8 years ago by ▴ 60
0
votes
8
replies
1.1k
views
Importing RSEM with tximport
tximport RSEM import error
updated 2.8 years ago by 40k • written 2.8 years ago by ▴ 60
2
votes
2
replies
635
views
RSEM for DESeq2 without abundance matrix
tximport deseq2 rsem
updated 2.8 years ago by 40k • written 2.8 years ago by ▴ 20
1
vote
3
replies
573
views
RSEM and Tximport
RSEM tximport deseq2
updated 3.0 years ago by 63k • written 3.0 years ago by • 0
4
votes
7
replies
2.7k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 3.0 years ago by 3.8k • written 3.0 years ago by • 0
0
votes
0
replies
527
views
Is the ballgownrsem function still supported?
ballgown rsem iranges
3.5 years ago • updated 3.4 years ago YH • 0
0
votes
6
replies
1.9k
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
4.7 years ago loliveira • 0
0
votes
0
replies
702
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
4.9 years ago kicheol.kim • 0
1
vote
0
replies
1.7k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
4.9 years ago kicheol.kim • 0
0
votes
1
reply
539
views
Using tximport on RSEM abundance date
rnaseq rsem tximport
updated 4.9 years ago by 40k • written 4.9 years ago by • 0
1
vote
4
replies
845
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 4.9 years ago by 40k • written 4.9 years ago by ▴ 50
0
votes
5
replies
930
views
countsFromAbundance for gene-level RSEM import in tximport
tximport rsem
updated 5.0 years ago by 40k • written 5.0 years ago by • 0
0
votes
0
replies
652
views
RSEM output in txtimport
RSEM txtimport
5.0 years ago gat2010 • 0
0
votes
8
replies
2.0k
views
Differences in gene length passed to DESeq2 by tximport reulted in different gene rankings
deseq2 tximport rsem saimon
updated 5.0 years ago by 40k • written 5.0 years ago by • 0
2
votes
18
replies
2.8k
views
Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
5.2 years ago stephan.emmrich ▴ 10
2
votes
2
replies
772
views
tximport failing at importing TPM instead of FPKM
tximport rnaseq rsem
updated 5.3 years ago by • 0 • written 5.3 years ago by • 0
3
votes
13
replies
1.6k
views
tximport's parameter for countsFromAbundance doesn't work
tximport rsem edger
5.3 years ago tim.ivanov.92 • 0
0
votes
1
reply
925
views
Data object format for deseq2
deseq2 R RSEM
updated 5.4 years ago by 40k • written 5.4 years ago by • 0
1
vote
2
replies
1.2k
views
RNA-seq read alignment best practices for low-input samples
limma differential gene expression rnaseq analysis alignment RSEM
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 10
3
votes
4
replies
2.8k
views
Importing RSEM transcript-level data using tximport
tximport rsem
updated 5.5 years ago by 40k • written 5.5 years ago by ▴ 10
2
votes
11
replies
3.4k
views
Tximport with RSEM error
RSEM
updated 5.6 years ago by ▴ 120 • written 5.6 years ago by ▴ 20
2
votes
7
replies
1.3k
views
Obtaining transcript names in RSEM
tximport rsem
updated 5.7 years ago by 40k • written 5.7 years ago by ▴ 20
0
votes
2
replies
921
views
Using RSEM reads for DESeq2
deseq2 rsem
updated 5.8 years ago by 40k • written 5.8 years ago by ▴ 10
3
votes
1
reply
1.2k
views
Filtering step in Differential analysis with RSEM values
rsem differential gene expression edger
updated 5.8 years ago by 47k • written 5.8 years ago by ▴ 110
0
votes
1
reply
1.5k
views
confusion with tximport options and resulting matrix
tximport rnaseq rsem limma voom
updated 5.9 years ago by 47k • written 5.9 years ago by • 0
1
vote
3
replies
2.0k
views
Differential analysis with RSEM normalized counts using limma without voom
limma differential gene expression tcga rsem
updated 5.9 years ago by 63k • written 5.9 years ago by ▴ 110
6
votes
5
replies
3.0k
views
Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
updated 6.1 years ago by 47k • written 6.1 years ago by ▴ 20
0
votes
0
replies
2.2k
views
How to normalize-transform rsem.genes.results of TCGA RNA-seq v2?
tcga rnaseq rsem R normalization
6.2 years ago panagiotis.mokos ▴ 40
0
votes
1
reply
1.5k
views
RSEM output in DeSeq2
RSEM deseq2 count matrix
updated 6.3 years ago by 40k • written 6.3 years ago by • 0
25
votes
37
replies
9.0k
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 6.4 years ago by 47k • written 6.4 years ago by ▴ 810
8
votes
5
replies
13k
views
Expected counts from RSEM in DESeq2
RSEM deseq2 expected_counts raw_counts
updated 23 months ago by 40k • written 6.4 years ago by ▴ 20
5
votes
9
replies
5.3k
views
Voom: need at least two non-NA values to interpolate
limma voom voom rsem fpkm
6.7 years ago komal.rathi ▴ 110
0
votes
8
replies
1.6k
views
Using Scran with RSEM/DEseq
scran normalization deseq2 rsem edger
6.8 years ago a.guerra • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Gordon Smyth 47k
Perhaps you are thinking of data analyses where the dependent variable is something other than expression itself. In the context of gene e…
Comment: Interpret plot from DiffBind by Chris • 0
If I want to find genes that are more open in diseased than control, I can filter out peaks that have highest log2Fold change like this, is…
Comment: Interpret plot from DiffBind by Chris • 0
Hi Rory. There are so many red dot above and below the blue line so it is hard to know which condition are more open, is that correct? Is 1…
Comment: Extract Limma Adjusted Values for Plotting by phelankj • 0
Thanks, on the normalized values using the same formula?
Answer: Extract Limma Adjusted Values for Plotting by James W. MacDonald 63k
You should use `removeBatchEffect` for that.
Votes
Answer: NA transcript values in my Txdb
Comment: Interpret plot from DiffBind
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
Answer: Interpret plot from DiffBind
Awards • All
Scholar to Mike Smith ★ 6.0k
Popular Question to Martin Morgan 25k
Teacher to deeenes ▴ 30
Popular Question to Hervé Pagès 16k
Popular Question to Gordon Smyth 47k
Locations • All
Republic of Ireland, 6 minutes ago
Russia, 7 minutes ago
WEHI, Melbourne, Australia, 8 minutes ago
United States, 15 minutes ago
United States, 37 minutes ago
Traffic: 183 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