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rnaseqdata
•
reset
22
votes
15
replies
7.3k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt
RNASeqData
R
updated 5 months ago by
Marie
▴ 10 • written 2.0 years ago by
Dina
▴ 50
5
votes
6
replies
514
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression
rnaseqGene
RNASeqData
12 weeks ago
Shaimaa Gamal
• 0
3
votes
3
replies
883
views
how to remove batch effects of RNA seq data based on continuous variables(like surrogate variables from sva package) using combatseq or limma (remove…
combatseq
RNASeqData
sva
limma
9 months ago
amnahsiddiqa
▴ 10
3
votes
4
replies
510
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
4 months ago
pl23
• 0
3
votes
3
replies
1.1k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM
RNASeqData
DEAnalysis
limma
7 months ago
Ethan Nguyen
• 0
3
votes
2
replies
654
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod
RNASeqData
edgeR
DESeq2
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
CDSPARKS
▴ 10
3
votes
5
replies
583
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 6 weeks ago by
Michael Love
41k • written 7 weeks ago by
sap275
▴ 10
2
votes
2
replies
383
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression
DESeq2
RNASeqData
RNASeq
StatisticalMethod
4 months ago
Manthos
• 0
2
votes
3
replies
1.0k
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect
sva
DESeq2
RNASeqData
limma
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
D-Bug
▴ 10
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 23 hours ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
2
votes
3
replies
1.1k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC
RNASeqData
sva
BatchEffect
updated 9 months ago by
ATpoint
★ 4.0k • written 9 months ago by
amnahsiddiqa
▴ 10
2
votes
3
replies
754
views
Two factor design including interaction effect with DESeq2 in R
DESeq2
RNASeqData
deseq2
ExperimentalDesign
updated 5 months ago by
swbarnes2
★ 1.3k • written 5 months ago by
Sam
• 0
2
votes
4
replies
640
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData
DifferentialExpression
SmallRNAData
DESeq2
6 months ago
Shihui
• 0
2
votes
5
replies
1.3k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR
RNASeq
RNASeqData
Bioconductor
written 13 months ago by
Rebekah
• 0
2
votes
1
reply
651
views
Using oligo or xps to read and convert RNA-seq data CEL file to txt file.
oligoData
DataImport
oligo
RNASeqData
convert
updated 9 months ago by
James W. MacDonald
65k • written 9 months ago by
rodj5201
• 0
1
vote
3
replies
312
views
DESeq2 analysis on time-series RNA experiment
RNASeqData
DESeq2
RNASeq
11 weeks ago
island
• 0
1
vote
1
reply
568
views
DESEQ2 differential expression for subsets of data?
RNASeqData
DESeq2
updated 9 months ago by
ATpoint
★ 4.0k • written 9 months ago by
amnahsiddiqa
▴ 10
1
vote
2
replies
635
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
4 months ago • updated 3 months ago
Levi
• 0
1
vote
1
reply
308
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 4 months ago by
ATpoint
★ 4.0k • written 4 months ago by
kaurprab
• 0
1
vote
1
reply
440
views
Best way to handle batch effects from difference Mice?
RNASeqData
BatchEffect
edgeR
limma
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
Sara
• 0
1
vote
9
replies
850
views
DESeq2 not replicable results
RNASeqData
DESeq2
updated 9 months ago by
Michael Love
41k • written 9 months ago by
Matteo
• 0
1
vote
1
reply
392
views
Multiple comparison using DESeq2
RNASeqData
RNASeq
DESeq2
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
fuqichen1
• 0
1
vote
1
reply
375
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData
DifferentialExpression
DESeq2
updated 3 months ago by
ATpoint
★ 4.0k • written 3 months ago by
kubracelikbas4
• 0
1
vote
2
replies
1.4k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon
IsoformSwitchAnalyzeR
tximport
RNASeqData
updated 8 months ago by
k.vitting.seerup
▴ 120 • written 8 months ago by
elva.gypsophila
▴ 10
1
vote
2
replies
408
views
RNASeq time course analysis, missing time points for control
RNASeqData
RnaSeqSampleSize
RNASeq
RNASeqPower
4 months ago
drewhaydensteele
• 0
1
vote
2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2
limma
RNASeq
RNASeqData
written 11 months ago by
informatician
• 0
1
vote
7
replies
791
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition
RNASeqData
limma
BulkRNAseq
RNASeq
updated 4 months ago by
Gordon Smyth
50k • written 6 months ago by
Gimena
• 0
1
vote
2
replies
500
views
I changed the reference in DGE contrasts by DESeq2, but the results changed just a bit and not in the sign of Log2FC (positive to negative and invers…
RNASeqData
DESeq2
updated 8 months ago by
Michael Love
41k • written 9 months ago by
mohammad.hossein.banabazi
• 0
1
vote
1
reply
431
views
bulk RNA-Seq batch correction
RNASeqData
rnaseqcomp
RNASeq
updated 7 months ago by
ATpoint
★ 4.0k • written 7 months ago by
jg0428
• 0
1
vote
1
reply
390
views
Deseq contrast question
RNASeqData
DESeq2
updated 10 months ago by
Michael Love
41k • written 10 months ago by
Hannah
▴ 10
0
votes
2
replies
608
views
MA plot for DESEq2 analysis
RNASeqData
DESeq2
5 months ago
RHEA
• 0
0
votes
1
reply
544
views
Controlling for covariates and identifying DEGs using DESeq2
RNASeqData
DESeq2
updated 9 months ago by
Michael Love
41k • written 9 months ago by
Abhishek Singh
▴ 20
0
votes
1
reply
317
views
Interaction terms in DESeq2
RNASeqData
RnaSeqSampleSize
DESeq2
updated 4 months ago by
James W. MacDonald
65k • written 4 months ago by
Mimi
• 0
0
votes
1
reply
384
views
Comparing RNASeq data from multiple studies
RNASeqData
RnaSeqSampleSize
RNASeqPower
RNASeq
updated 6 months ago by
Basti
▴ 760 • written 6 months ago by
Luke
• 0
0
votes
1
reply
353
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData
DESeq2
updated 5 months ago by
Wolfgang Huber
★ 13k • written 5 months ago by
meroy
• 0
0
votes
3
replies
655
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData
DESeq2
4 months ago
Oenone
• 0
0
votes
2
replies
316
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData
STRINGdb
DifferentialExpression
GraphAndNetwork
Network
4 months ago
Luca
• 0
0
votes
2
replies
981
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData
Rsubread
mapping
featurecounts
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
vitoriastavis
• 0
0
votes
0
replies
312
views
BubbleGUM for multi group comparison of gene set enrichment
RNASeqData
GeneSetEnrichment
multiGSEA
9 months ago
sonal
• 0
0
votes
4
replies
628
views
filtering out lowly expressed genes by groups
RNASeqData
DESeq2
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
sohail.mbio
▴ 10
0
votes
0
replies
374
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData
BatchEffect
sva
9 months ago
amnahsiddiqa
▴ 10
0
votes
6
replies
748
views
Questionable limma results for differential expression on RNA-seq
RNASeqData
DifferentialExpression
limma
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
gld-bioinf
• 0
0
votes
1
reply
623
views
Can I transform already normalized rna-seq data with Z-score?
Z-score
RNASeqData
Deseq
DESeq2
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
khaserdene99
• 0
0
votes
1
reply
317
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData
DifferentialExpression
DESeq2
updated 4 months ago by
Michael Love
41k • written 5 months ago by
Pez
▴ 10
0
votes
0
replies
188
views
Differential expression analysis between different species
DEG
RNASeqData
DifferentialExpression
SCBN
RNASeq
9 weeks ago
Abril
• 0
0
votes
1
reply
487
views
Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2
RNASeqData
edgeR
limma
DifferentialExpression
updated 7 months ago by
ATpoint
★ 4.0k • written 7 months ago by
Sep
• 0
0
votes
0
replies
516
views
News:
Course - Network Analysis in Systems Biology with R/Bioconductor
Bioconductor
Network
RNASeqData
SystemsBiology
9 months ago
info
▴ 10
0
votes
2
replies
864
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 18 hours ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
0
votes
1
reply
488
views
Design formula for genotype-specific condition effects using ~group in the design
RNASeqData
DifferentialExpression
DESeq2
updated 10 months ago by
Michael Love
41k • written 10 months ago by
james.zhang20
• 0
0
votes
2
replies
552
views
RNA seq differential expression analysis
DEGseq
RNASeqData
limma
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
Shaimaa Gamal
• 0
50 results • Page
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Answer: DESEQ2 output gives multiple groups when only 2 groups are present
by
ATpoint
★ 4.0k
In the first PCA plot there is almost certainly some hidden character like whitespaces in the column from colData that encodes this group. …
Answer: A ComBat-seq issue: the covariates are confounded
by
ATpoint
★ 4.0k
```r > table(batch, group) group batch egfr gfp her2 1 0 12 5 2 6 6 0 ``` All of her2 is batch2, all of egfr i…
Comment: DESeq2 setting significant p-value
by
Dev
• 0
after running DESeq2 does it sort the value on the basis of pvalue, or anything, or does it give the data back in the input format I have …
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
But wouldn't this result in a different gene set for each analysis stratification? How can you then compare if maybe gene x comes up in Tim…
Comment: Reading huge bismark coverage files using bbseq::read.bismark
by
jacques.imbert
• 0
Hello, Using nThread = 1L fixed the issue. Thank you for your time and help.
Votes
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
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