Showing : RSEM • reset
9
votes
5
replies
16k
views
Expected counts from RSEM in DESeq2
RSEM deseq2 expected_counts raw_counts
updated 2.8 years ago by 41k • written 7.3 years ago by ▴ 30
25
votes
37
replies
11k
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 7.3 years ago by 50k • written 7.3 years ago by ▴ 830
5
votes
9
replies
5.9k
views
Voom: need at least two non-NA values to interpolate
limma voom voom rsem fpkm
7.6 years ago komal.rathi ▴ 120
6
votes
13
replies
5.1k
views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
updated 21 months ago by 50k • written 3.7 years ago by ▴ 60
2
votes
11
replies
4.3k
views
Tximport with RSEM error
RSEM
updated 6.5 years ago by ▴ 120 • written 6.5 years ago by ▴ 20
6
votes
4
replies
4.1k
views
RSEM expected counts to limma-voom
limma voom rsem
updated 7.8 years ago by 50k • written 7.8 years ago by ▴ 90
4
votes
7
replies
3.9k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 3.9 years ago by ★ 3.9k • written 3.9 years ago by • 0
6
votes
5
replies
3.8k
views
Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
updated 7.0 years ago by 50k • written 7.0 years ago by ▴ 20
3
votes
4
replies
3.7k
views
Importing RSEM transcript-level data using tximport
tximport rsem
updated 6.4 years ago by 41k • written 6.4 years ago by ▴ 10
2
votes
18
replies
3.4k
views
Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
6.1 years ago stephan.emmrich ▴ 10
1
vote
3
replies
2.6k
views
Differential analysis with RSEM normalized counts using limma without voom
limma differential gene expression tcga rsem
updated 6.8 years ago by 65k • written 6.8 years ago by ▴ 110
0
votes
0
replies
2.5k
views
How to normalize-transform rsem.genes.results of TCGA RNA-seq v2?
tcga rnaseq rsem R normalization
7.1 years ago panagiotis.mokos ▴ 40
0
votes
8
replies
2.5k
views
Differences in gene length passed to DESeq2 by tximport reulted in different gene rankings
deseq2 tximport rsem saimon
updated 5.9 years ago by 41k • written 5.9 years ago by • 0
0
votes
6
replies
2.5k
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
5.6 years ago loliveira • 0
3
votes
13
replies
2.4k
views
tximport's parameter for countsFromAbundance doesn't work
tximport rsem edger
6.2 years ago tim.ivanov.92 • 0
6
votes
6
replies
2.3k
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2 VST rsem tximport
3.4 years ago svlachavas ▴ 830
4
votes
5
replies
2.2k
views
Which is the best type of data for correlation or survival analysis
TPM RNASeq RSEM DESeq2
updated 20 months ago by 41k • written 20 months ago by ▴ 10
1
vote
3
replies
2.1k
views
DESeq2 size factors estimation after RSEM quantification
deseq2 tximport rsem estimatesizefactors
8.0 years ago Hugo Varet ▴ 80
1
vote
0
replies
2.0k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
5.8 years ago kicheol.kim • 0
2
votes
7
replies
2.0k
views
Obtaining transcript names in RSEM
tximport rsem
updated 6.6 years ago by 41k • written 6.6 years ago by ▴ 20
0
votes
8
replies
2.0k
views
Using Scran with RSEM/DEseq
scran normalization deseq2 rsem edger
7.7 years ago a.guerra • 0
5
votes
9
replies
1.8k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
21 months ago Yang Shi ▴ 10
0
votes
8
replies
1.8k
views
Importing RSEM with tximport
tximport RSEM import error
updated 3.7 years ago by 41k • written 3.7 years ago by ▴ 60
0
votes
1
reply
1.8k
views
RSEM output in DeSeq2
RSEM deseq2 count matrix
updated 7.2 years ago by 41k • written 7.2 years ago by • 0
0
votes
1
reply
1.8k
views
confusion with tximport options and resulting matrix
tximport rnaseq rsem limma voom
updated 6.8 years ago by 50k • written 6.8 years ago by • 0
5
votes
6
replies
1.7k
views
Removing the duplicated genes before limma::voom by using limma::avereps
RSEM avereps voom limma RNASeq
21 months ago Yang Shi ▴ 10
4
votes
7
replies
1.7k
views
assigning differential exons to trascripts
dexseq rsem differential exon usage differential gene expression
updated 7.8 years ago by 65k • written 7.8 years ago by ★ 1.5k
1
vote
2
replies
1.7k
views
RNA-seq read alignment best practices for low-input samples
limma differential gene expression rnaseq analysis alignment RSEM
updated 6.3 years ago by ★ 28k • written 6.4 years ago by ▴ 10
0
votes
2
replies
1.5k
views
Use of RSEM counts in WGCNA
rsemmed RSEM WGCNA
3.4 years ago harelarik ▴ 60
2
votes
8
replies
1.5k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
22 months ago Kelen ▴ 10
3
votes
1
reply
1.5k
views
Filtering step in Differential analysis with RSEM values
rsem differential gene expression edger
updated 6.7 years ago by 50k • written 6.7 years ago by ▴ 110
0
votes
2
replies
1.4k
views
How well does "Trinity-Differential-Expression" work on normalized raw counts without RSEM abundance of estimation
Trinity DifferentialExpression RSEM RNAseq edgeR
3.4 years ago harelarik ▴ 60
2
votes
4
replies
1.3k
views
Doing normalization when using voom for DEG analysis?
limma RSEM voom Normalization
21 months ago Yang Shi ▴ 10
1
vote
4
replies
1.3k
views
TCGA data analysis
RSEM
3.0 years ago lily ▴ 20
0
votes
5
replies
1.3k
views
countsFromAbundance for gene-level RSEM import in tximport
tximport rsem
updated 5.8 years ago by 41k • written 5.8 years ago by • 0
1
vote
4
replies
1.3k
views
How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2 when DEGs
limma edgeR RSEM
updated 13 months ago by 50k • written 13 months ago by ▴ 10
0
votes
2
replies
1.3k
views
Using RSEM reads for DESeq2
deseq2 rsem
updated 6.6 years ago by 41k • written 6.6 years ago by ▴ 10
0
votes
1
reply
1.3k
views
Data object format for deseq2
deseq2 R RSEM
updated 6.3 years ago by 41k • written 6.3 years ago by • 0
2
votes
3
replies
1.2k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
17 months ago • updated 16 months ago mohammedtoufiq91 ▴ 10
0
votes
3
replies
1.2k
views
Differential Expression Analysis on RNAseq - RSEM expected_count from UCSC RNA-Seq toil recompute
DESeq2 Toil RSEM
18 months ago Niveditha ▴ 20
1
vote
4
replies
1.2k
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 5.8 years ago by 41k • written 5.8 years ago by ▴ 50
2
votes
2
replies
1.1k
views
tximport failing at importing TPM instead of FPKM
tximport rnaseq rsem
updated 6.2 years ago by • 0 • written 6.2 years ago by • 0
1
vote
4
replies
1.0k
views
tximport abundanceCol parameter not functioning for rsem data
tximport rsem transcript abundance TPM FPKM
updated 3.5 years ago by 41k • written 3.6 years ago by • 0
0
votes
0
replies
958
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
5.8 years ago kicheol.kim • 0
2
votes
2
replies
955
views
RSEM for DESeq2 without abundance matrix
tximport deseq2 rsem
updated 3.7 years ago by 41k • written 3.7 years ago by ▴ 20
0
votes
1
reply
933
views
tximport error importing expected counts file from RSEM
RSEM tximport
updated 3.3 years ago by 41k • written 3.3 years ago by • 0
1
vote
3
replies
869
views
Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue Spati RSEM deno DEseq2
updated 10 months ago by • 0 • written 11 months ago by • 0
0
votes
0
replies
861
views
RSEM output in txtimport
RSEM txtimport
5.9 years ago gat2010 • 0
1
vote
3
replies
842
views
RSEM and Tximport
RSEM tximport deseq2
updated 3.9 years ago by 65k • written 3.9 years ago by • 0
0
votes
1
reply
811
views
Using tximport on RSEM abundance date
rnaseq rsem tximport
updated 5.8 years ago by 41k • written 5.8 years ago by • 0
50 results • Page 1 of 1
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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