Showing : RSEM • reset
0
votes
4
replies
562
views
Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
5 months ago NB • 0
0
votes
1
reply
875
views
tximport error with rsem files
rsem tximport
updated 16 months ago by ★ 4.8k • written 16 months ago by • 0
1
vote
4
replies
1.4k
views
Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue Spati RSEM deno DEseq2
written 23 months ago by • 0
1
vote
4
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2.3k
views
How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2 when DEGs
limma edgeR RSEM
updated 2.1 years ago by 52k • written 2.1 years ago by ▴ 10
1
vote
2
replies
1.0k
views
Differential expression analysis based on EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2
DESeq2 limma edgeR RSEM
2.1 years ago Yang Shi ▴ 10
2
votes
3
replies
1.9k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
2.4 years ago mohammedtoufiq91 ▴ 10
0
votes
3
replies
2.1k
views
Differential Expression Analysis on RNAseq - RSEM expected_count from UCSC RNA-Seq toil recompute
DESeq2 Toil RSEM
2.5 years ago Niveditha ▴ 20
4
votes
5
replies
3.1k
views
Which is the best type of data for correlation or survival analysis
TPM RNASeq RSEM DESeq2
updated 2.7 years ago by 43k • written 2.7 years ago by ▴ 10
5
votes
9
replies
2.6k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
2.7 years ago Yang Shi ▴ 10
5
votes
6
replies
2.4k
views
Removing the duplicated genes before limma::voom by using limma::avereps
RSEM avereps voom limma RNASeq
2.8 years ago Yang Shi ▴ 10
2
votes
4
replies
2.4k
views
Doing normalization when using voom for DEG analysis?
limma RSEM voom Normalization
2.8 years ago Yang Shi ▴ 10
2
votes
8
replies
2.2k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
2.8 years ago Kelen ▴ 10
0
votes
0
replies
931
views
Proper normalization of batch effected corrected raw rsem rnaseq values for downstream unsupervised analyses
limma RNASeq rsem Normalization
3.5 years ago svlachavas ▴ 840
1
vote
4
replies
1.8k
views
TCGA data analysis
RSEM
4.0 years ago lily ▴ 20
0
votes
1
reply
1.2k
views
tximport error importing expected counts file from RSEM
RSEM tximport
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
0
votes
2
replies
1.8k
views
How well does "Trinity-Differential-Expression" work on normalized raw counts without RSEM abundance of estimation
Trinity DifferentialExpression RSEM RNAseq edgeR
4.4 years ago harelarik ▴ 60
6
votes
6
replies
2.8k
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2 VST rsem tximport
4.4 years ago svlachavas ▴ 840
0
votes
2
replies
1.9k
views
Use of RSEM counts in WGCNA
rsemmed RSEM WGCNA
4.4 years ago harelarik ▴ 60
1
vote
4
replies
1.4k
views
tximport abundanceCol parameter not functioning for rsem data
tximport rsem transcript abundance TPM FPKM
updated 4.5 years ago by 43k • written 4.6 years ago by • 0
6
votes
13
replies
7.2k
views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
updated 2.8 years ago by 52k • written 4.7 years ago by ▴ 60
0
votes
8
replies
2.5k
views
Importing RSEM with tximport
tximport RSEM import error
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 60
2
votes
2
replies
1.3k
views
RSEM for DESeq2 without abundance matrix
tximport deseq2 rsem
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 20
1
vote
3
replies
1.1k
views
RSEM and Tximport
RSEM tximport deseq2
updated 4.9 years ago by 68k • written 4.9 years ago by • 0
4
votes
7
replies
5.4k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by • 0
0
votes
0
replies
1.1k
views
Is the ballgownrsem function still supported?
ballgown rsem iranges
5.4 years ago • updated 5.3 years ago YH • 0
0
votes
6
replies
2.9k
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
6.6 years ago loliveira • 0
0
votes
0
replies
1.2k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
6.8 years ago kicheol.kim • 0
1
vote
0
replies
2.3k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
6.8 years ago kicheol.kim • 0
0
votes
1
reply
1.0k
views
Using tximport on RSEM abundance date
rnaseq rsem tximport
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
1
vote
4
replies
1.6k
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 6.8 years ago by 43k • written 6.8 years ago by ▴ 50
0
votes
5
replies
1.7k
views
countsFromAbundance for gene-level RSEM import in tximport
tximport rsem
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
0
votes
0
replies
1.1k
views
RSEM output in txtimport
RSEM txtimport
6.9 years ago gat2010 • 0
0
votes
8
replies
3.1k
views
Differences in gene length passed to DESeq2 by tximport reulted in different gene rankings
deseq2 tximport rsem saimon
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
2
votes
18
replies
4.0k
views
Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
7.1 years ago stephan.emmrich ▴ 10
2
votes
2
replies
1.4k
views
tximport failing at importing TPM instead of FPKM
tximport rnaseq rsem
updated 7.2 years ago by • 0 • written 7.2 years ago by • 0
3
votes
13
replies
3.0k
views
tximport's parameter for countsFromAbundance doesn't work
tximport rsem edger
7.2 years ago tim.ivanov.92 • 0
0
votes
1
reply
1.6k
views
Data object format for deseq2
deseq2 R RSEM
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
1
vote
2
replies
2.4k
views
RNA-seq read alignment best practices for low-input samples
limma differential gene expression rnaseq analysis alignment RSEM
updated 7.3 years ago by ★ 28k • written 7.4 years ago by ▴ 10
3
votes
4
replies
4.5k
views
Importing RSEM transcript-level data using tximport
tximport rsem
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 10
2
votes
13
replies
5.6k
views
Tximport with RSEM error
RSEM
updated 5 months ago by 43k • written 7.5 years ago by ▴ 20
2
votes
7
replies
2.6k
views
Obtaining transcript names in RSEM
tximport rsem
updated 7.6 years ago by 43k • written 7.6 years ago by ▴ 20
1
vote
2
replies
1.9k
views
Using RSEM reads for DESeq2
deseq2 rsem
updated 7.6 years ago by 43k • written 7.6 years ago by ▴ 10
3
votes
1
reply
1.8k
views
Filtering step in Differential analysis with RSEM values
rsem differential gene expression edger
updated 7.7 years ago by 52k • written 7.7 years ago by ▴ 120
0
votes
1
reply
2.1k
views
confusion with tximport options and resulting matrix
tximport rnaseq rsem limma voom
updated 7.8 years ago by 52k • written 7.8 years ago by • 0
1
vote
3
replies
3.2k
views
Differential analysis with RSEM normalized counts using limma without voom
limma differential gene expression tcga rsem
updated 7.8 years ago by 68k • written 7.8 years ago by ▴ 120
6
votes
5
replies
4.6k
views
Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
updated 8.0 years ago by 52k • written 8.0 years ago by ▴ 20
0
votes
0
replies
2.9k
views
How to normalize-transform rsem.genes.results of TCGA RNA-seq v2?
tcga rnaseq rsem R normalization
8.1 years ago panagiotis.mokos ▴ 40
0
votes
1
reply
2.2k
views
RSEM output in DeSeq2
RSEM deseq2 count matrix
updated 8.2 years ago by 43k • written 8.2 years ago by • 0
25
votes
37
replies
13k
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 8.3 years ago by 52k • written 8.3 years ago by ▴ 840
10
votes
5
replies
19k
views
Expected counts from RSEM in DESeq2
RSEM deseq2 expected_counts raw_counts
updated 3.8 years ago by 43k • written 8.3 years ago by ▴ 30
50 results • Page 1 of 1
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Replies
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by donnycrimson • 0
Have you considered streamlining how you handle data input to mitigate these issues. It might help to define the parameters more strictly …
Comment: CluserProfiler message "No gene can be mapped" by Carolina • 0
There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…
Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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