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 • 0 • written 6 months ago by • 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 48k • written 8 months ago by ▴ 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 41k • written 16 months ago by ▴ 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 41k • written 2.9 years ago by • 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 41k • written 3.2 years ago by • 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 48k • written 3.3 years ago by ▴ 60
0
votes
8
replies
1.5k
views
Importing RSEM with tximport
tximport RSEM import error
updated 3.3 years ago by 41k • written 3.3 years ago by ▴ 60
2
votes
2
replies
829
views
RSEM for DESeq2 without abundance matrix
tximport deseq2 rsem
updated 3.3 years ago by 41k • written 3.3 years ago by ▴ 20
1
vote
3
replies
726
views
RSEM and Tximport
RSEM tximport deseq2
updated 3.5 years ago by 64k • written 3.5 years ago by • 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 3.9k • written 3.5 years ago by • 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 41k • written 5.4 years ago by • 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 41k • written 5.4 years ago by ▴ 50
0
votes
5
replies
1.1k
views
countsFromAbundance for gene-level RSEM import in tximport
tximport rsem
updated 5.5 years ago by 41k • written 5.5 years ago by • 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 41k • written 5.5 years ago by • 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 • 0 • written 5.8 years ago by • 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 41k • written 5.9 years ago by • 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 ★ 28k • written 6.0 years ago by ▴ 10
3
votes
4
replies
3.2k
views
Importing RSEM transcript-level data using tximport
tximport rsem
updated 6.0 years ago by 41k • written 6.0 years ago by ▴ 10
2
votes
11
replies
3.9k
views
Tximport with RSEM error
RSEM
updated 6.1 years ago by ▴ 120 • written 6.1 years ago by ▴ 20
2
votes
7
replies
1.7k
views
Obtaining transcript names in RSEM
tximport rsem
updated 6.2 years ago by 41k • written 6.2 years ago by ▴ 20
0
votes
2
replies
1.1k
views
Using RSEM reads for DESeq2
deseq2 rsem
updated 6.3 years ago by 41k • written 6.3 years ago by ▴ 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 48k • written 6.3 years ago by ▴ 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 48k • written 6.4 years ago by • 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 64k • written 6.4 years ago by ▴ 110
6
votes
5
replies
3.5k
views
Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
updated 6.6 years ago by 48k • written 6.6 years ago by ▴ 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 41k • written 6.8 years ago by • 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 48k • written 6.9 years ago by ▴ 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 41k • written 6.9 years ago by ▴ 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?
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