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0
votes
1
answer
115
views
1
answer
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 deseq2 rsem written 7 weeks ago by loliveira • 0
0
votes
0
answers
81
views
0
answers
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
iranges ballgown rsem written 3 months ago by kicheol.kim • 0
1
vote
0
answers
143
views
0
answers
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
iranges ballgown rsem written 4 months ago by kicheol.kim • 0
0
votes
1
answer
87
views
1
answer
Using tximport on RSEM abundance date
rnaseq tximport rsem written 4 months ago by raeganlynn123 • 0 • updated 4 months ago by Michael Love ♦ 20k
1
vote
1
answer
136
views
1
answer
DE analysis of orthologs with varying sequence lengths using RSEM+tximport+DEseq2: normalization for sequence length?
deseq2 differential expression tximport rsem sequence length normalization written 4 months ago by al-ash • 20 • updated 4 months ago by Michael Love ♦ 20k
0
votes
1
answer
118
views
1
answer
countsFromAbundance for gene-level RSEM import in tximport
tximport rsem written 4 months ago by celi0001 • 0 • updated 4 months ago by Michael Love ♦ 20k
0
votes
0
answers
109
views
0
answers
RSEM output in txtimport
rsem txtimport written 5 months ago by gat2010 • 0
0
votes
1
answer
315
views
1
answer
Differences in gene length passed to DESeq2 by tximport reulted in different gene rankings
deseq2 tximport rsem saimon written 5 months ago by LD • 0 • updated 5 months ago by Michael Love ♦ 20k
0
votes
1
answer
420
views
1
answer
Using tximport on rsem files produces error while trying to read in files
rnaseq R tpm tximport rsem written 7 months ago by stephan.emmrich • 0
2
votes
1
answer
158
views
1
answer
tximport failing at importing TPM instead of FPKM
rnaseq tximport rsem written 8 months ago by fresard.laure • 0 • updated 8 months ago by rosabellascottgm • 0
3
votes
2
answers
326
views
2
answers
tximport's parameter for countsFromAbundance doesn't work
edger tximport rsem written 9 months ago by tim.ivanov.92 • 0
0
votes
1
answer
217
views
1
answer
Data object format for deseq2
deseq2 R rsem written 10 months ago by tim.ivanov.92 • 0 • updated 10 months ago by Michael Love ♦ 20k
1
vote
1
answer
380
views
1
answer
RNA-seq read alignment best practices for low-input samples
alignment limma differential gene expression rsem rnaseq analysis written 10 months ago by goldberg.jm • 10 • updated 10 months ago by Aaron Lun • 21k
1
vote
1
answer
509
views
1
answer
Importing RSEM transcript-level data using tximport
tximport rsem written 11 months ago by Patrick Kimes • 0 • updated 11 months ago by Michael Love ♦ 20k
1
vote
1
answer
531
views
1
answer
Tximport with RSEM error
rsem written 12 months ago by hs.lansdell • 10 • updated 12 months ago by k.vitting.seerup • 30
2
votes
1
answer
349
views
1
answer
Obtaining transcript names in RSEM
tximport rsem written 13 months ago by deena • 10 • updated 13 months ago by Michael Love ♦ 20k
0
votes
1
answer
377
views
1
answer
Using RSEM reads for DESeq2
deseq2 rsem written 14 months ago by deeptiptl74 • 0 • updated 14 months ago by Michael Love ♦ 20k
3
votes
1
answer
575
views
1
answer
Filtering step in Differential analysis with RSEM values
edger differential gene expression rsem written 15 months ago by Biologist • 70 • updated 15 months ago by Gordon Smyth ♦ 35k
0
votes
1
answer
790
views
1
answer
confusion with tximport options and resulting matrix
rnaseq limma voom tximport rsem written 15 months ago by arubio • 0 • updated 15 months ago by Gordon Smyth ♦ 35k
1
vote
1
answer
471
views
1
answer
Differential analysis with RSEM normalized counts using limma without voom
limma differential gene expression tcga rsem written 16 months ago by Biologist • 70 • updated 16 months ago by James W. MacDonald ♦ 48k
5
votes
1
answer
918
views
1
answer
Clustering differential expression results from voomWithQualityWeights
limma edger rna rsem written 19 months ago by hrishi27n • 0 • updated 19 months ago by Gordon Smyth ♦ 35k
0
votes
0
answers
963
views
0
answers
How to normalize-transform rsem.genes.results of TCGA RNA-seq v2?
rnaseq normalization R tcga rsem written 20 months ago by panagiotis.mokos • 20
0
votes
1
answer
663
views
1
answer
RSEM output in DeSeq2
deseq2 count matrix rsem written 21 months ago by kmeusemann • 0 • updated 21 months ago by Michael Love ♦ 20k
24
votes
3
answers
2.7k
views
9 follow
3
answers
Possible ways of performing differential gene expression and analysis of RNA-Seq data from normalized counts of RSEM software
rnaseq normalization edger tcga rsem written 22 months ago by svlachavas • 610 • updated 22 months ago by Gordon Smyth ♦ 35k
0
votes
1
answer
2.9k
views
1
answer
Expected counts from RSEM in DESeq2
deseq2 rsem expected_counts raw_counts written 22 months ago by chudar.chudar • 0 • updated 22 months ago by Michael Love ♦ 20k
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