Showing : rsem • reset
0
votes
4
replies
382
views
Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
28 days ago NB • 0
0
votes
1
reply
705
views
tximport error with rsem files
rsem tximport
updated 12 months ago by ★ 4.6k • written 12 months ago by • 0
1
vote
4
replies
1.3k
views
Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue Spati RSEM deno DEseq2
written 19 months ago by • 0
1
vote
4
replies
2.0k
views
How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2 when DEGs
limma edgeR RSEM
updated 21 months ago by 52k • written 21 months ago by ▴ 10
1
vote
2
replies
916
views
Differential expression analysis based on EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2
DESeq2 limma edgeR RSEM
21 months ago Yang Shi ▴ 10
2
votes
3
replies
1.7k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
2.1 years ago mohammedtoufiq91 ▴ 10
0
votes
3
replies
1.8k
views
Differential Expression Analysis on RNAseq - RSEM expected_count from UCSC RNA-Seq toil recompute
DESeq2 Toil RSEM
2.2 years ago • updated 2.1 years ago Niveditha ▴ 20
4
votes
5
replies
2.8k
views
Which is the best type of data for correlation or survival analysis
TPM RNASeq RSEM DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 10
5
votes
9
replies
2.4k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
2.4 years ago Yang Shi ▴ 10
5
votes
6
replies
2.1k
views
Removing the duplicated genes before limma::voom by using limma::avereps
RSEM avereps voom limma RNASeq
2.4 years ago Yang Shi ▴ 10
2
votes
4
replies
2.0k
views
Doing normalization when using voom for DEG analysis?
limma RSEM voom Normalization
2.4 years ago Yang Shi ▴ 10
2
votes
8
replies
2.0k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
2.5 years ago Kelen ▴ 10
0
votes
0
replies
858
views
Proper normalization of batch effected corrected raw rsem rnaseq values for downstream unsupervised analyses
limma RNASeq rsem Normalization
3.1 years ago svlachavas ▴ 840
1
vote
4
replies
1.6k
views
TCGA data analysis
RSEM
3.7 years ago lily ▴ 20
0
votes
1
reply
1.1k
views
tximport error importing expected counts file from RSEM
RSEM tximport
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
0
votes
2
replies
1.6k
views
How well does "Trinity-Differential-Expression" work on normalized raw counts without RSEM abundance of estimation
Trinity DifferentialExpression RSEM RNAseq edgeR
4.0 years ago harelarik ▴ 60
6
votes
6
replies
2.7k
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2 VST rsem tximport
4.1 years ago svlachavas ▴ 840
0
votes
2
replies
1.8k
views
Use of RSEM counts in WGCNA
rsemmed RSEM WGCNA
4.1 years ago harelarik ▴ 60
1
vote
4
replies
1.3k
views
tximport abundanceCol parameter not functioning for rsem data
tximport rsem transcript abundance TPM FPKM
updated 4.1 years ago by 43k • written 4.3 years ago by • 0
6
votes
13
replies
6.4k
views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
updated 2.4 years ago by 52k • written 4.3 years ago by ▴ 60
0
votes
8
replies
2.3k
views
Importing RSEM with tximport
tximport RSEM import error
updated 4.3 years ago by 43k • written 4.3 years ago by ▴ 60
2
votes
2
replies
1.2k
views
RSEM for DESeq2 without abundance matrix
tximport deseq2 rsem
updated 4.4 years ago by 43k • written 4.4 years ago by ▴ 20
1
vote
3
replies
1.0k
views
RSEM and Tximport
RSEM tximport deseq2
updated 4.5 years ago by 67k • written 4.5 years ago by • 0
4
votes
7
replies
4.7k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by • 0
0
votes
0
replies
1.0k
views
Is the ballgownrsem function still supported?
ballgown rsem iranges
5.0 years ago YH • 0
0
votes
6
replies
2.8k
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
6.2 years ago loliveira • 0
0
votes
0
replies
1.1k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
6.4 years ago kicheol.kim • 0
1
vote
0
replies
2.2k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
6.5 years ago • updated 6.4 years ago kicheol.kim • 0
0
votes
1
reply
960
views
Using tximport on RSEM abundance date
rnaseq rsem tximport
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
1
vote
4
replies
1.5k
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 6.5 years ago by 43k • written 6.5 years ago by ▴ 50
0
votes
5
replies
1.6k
views
countsFromAbundance for gene-level RSEM import in tximport
tximport rsem
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
votes
0
replies
1.0k
views
RSEM output in txtimport
RSEM txtimport
6.6 years ago gat2010 • 0
0
votes
8
replies
2.9k
views
Differences in gene length passed to DESeq2 by tximport reulted in different gene rankings
deseq2 tximport rsem saimon
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
2
votes
18
replies
3.8k
views
Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
6.7 years ago stephan.emmrich ▴ 10
2
votes
2
replies
1.3k
views
tximport failing at importing TPM instead of FPKM
tximport rnaseq rsem
updated 6.8 years ago by • 0 • written 6.8 years ago by • 0
3
votes
13
replies
2.7k
views
tximport's parameter for countsFromAbundance doesn't work
tximport rsem edger
6.9 years ago tim.ivanov.92 • 0
0
votes
1
reply
1.4k
views
Data object format for deseq2
deseq2 R RSEM
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
1
vote
2
replies
2.1k
views
RNA-seq read alignment best practices for low-input samples
limma differential gene expression rnaseq analysis alignment RSEM
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 10
3
votes
4
replies
4.2k
views
Importing RSEM transcript-level data using tximport
tximport rsem
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 10
2
votes
13
replies
5.2k
views
Tximport with RSEM error
RSEM
updated 5 weeks ago by 43k • written 7.2 years ago by ▴ 20
2
votes
7
replies
2.4k
views
Obtaining transcript names in RSEM
tximport rsem
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 20
1
vote
2
replies
1.7k
views
Using RSEM reads for DESeq2
deseq2 rsem
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
3
votes
1
reply
1.7k
views
Filtering step in Differential analysis with RSEM values
rsem differential gene expression edger
updated 7.4 years ago by 52k • written 7.4 years ago by ▴ 120
0
votes
1
reply
2.0k
views
confusion with tximport options and resulting matrix
tximport rnaseq rsem limma voom
updated 7.4 years ago by 52k • written 7.4 years ago by • 0
1
vote
3
replies
2.9k
views
Differential analysis with RSEM normalized counts using limma without voom
limma differential gene expression tcga rsem
updated 7.4 years ago by 67k • written 7.4 years ago by ▴ 120
6
votes
5
replies
4.3k
views
Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
updated 7.7 years ago by 52k • written 7.7 years ago by ▴ 20
0
votes
0
replies
2.8k
views
How to normalize-transform rsem.genes.results of TCGA RNA-seq v2?
tcga rnaseq rsem R normalization
7.8 years ago panagiotis.mokos ▴ 40
0
votes
1
reply
2.1k
views
RSEM output in DeSeq2
RSEM deseq2 count matrix
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
25
votes
37
replies
12k
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 7.9 years ago by 52k • written 7.9 years ago by ▴ 840
10
votes
5
replies
18k
views
Expected counts from RSEM in DESeq2
RSEM deseq2 expected_counts raw_counts
updated 3.5 years ago by 43k • written 8.0 years ago by ▴ 30
50 results • Page 1 of 1
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Replies
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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