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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
1
vote
12
replies
2.3k
views
Is there a need or general principle/rule to assess whether the data types/distribution etc is suitable for limma R package to derive differential fe…
limma
highthroughputassays
R
updated 12 weeks ago by
Mary
• 0 • written 2.5 years ago by
Ming
▴ 380
8
votes
11
replies
11k
views
R: error while reading .h5 files from R using rdhf5 package
rhdf5
r
hdf5
updated 11 months ago by
Yijing
• 0 • written 6.8 years ago by
him4u324
▴ 10
10
votes
10
replies
6.3k
views
biomaRt not working - lazy table error
error
lazy
R
biomaRt
table
updated 27 days ago by
juo5
• 0 • written 5 months ago by
Abhishek
▴ 10
0
votes
10
replies
782
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R
BioMart
biomaRt
5 months ago • updated 6 weeks ago
ScafioRuo
• 0
4
votes
8
replies
2.1k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2
limma
Normalization
R
updated 10 months ago by
Gordon Smyth
50k • written 16 months ago by
Sabiha
▴ 20
4
votes
7
replies
13k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 7 months ago by
Gordon Smyth
50k • written 21 months ago by
Mohamed
▴ 30
0
votes
6
replies
8.6k
views
No gene can be mapped error with clusterprofiler
clusterprofiler
r
updated 3 months ago by
Guido Hooiveld
★ 3.9k • written 7.3 years ago by
prp291
• 0
4
votes
5
replies
1.9k
views
time course microarray data ArrayExpress database
R
GillespieColin
ArrayExpress
import
TimeSeriesExperiment
updated 6 months ago by
jacorvar
▴ 40 • written 18 months ago by
eraldagjika
▴ 20
0
votes
5
replies
9.2k
views
tximport all(file.exists(files)) is not TRUE
bioconductor
tximport
rnaseq
R
updated 29 days ago by
Eva
• 0 • written 7.6 years ago by
ctl
• 0
1
vote
5
replies
2.1k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo
microarray
r
bioconductor
written 9.2 years ago by
chandlerjd58
▴ 10
2
votes
5
replies
1.3k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R
edgeR
RNASeq
9 months ago • updated 8 months ago
mohammedtoufiq91
▴ 10
7
votes
5
replies
6.8k
views
biomaRt server error, and mirrors do not help
ensembl
biomaRt
R
updated 6 months ago by
Ke
• 0 • written 23 months ago by
kieran.short
▴ 40
0
votes
4
replies
865
views
Combine RNA-seq
BatchEffect
R
rnaseq
updated 11 months ago by
swbarnes2
★ 1.3k • written 11 months ago by
Young Tae
• 0
0
votes
4
replies
323
views
limma with interaction term
R
biostatistics
limma
Epigenetics
9 weeks ago • updated 7 weeks ago
Jitendra
▴ 10
2
votes
4
replies
1.6k
views
make TxDb from list of genes
R
maketxdbfrombiomart
maketxdbfromgranges
rstudio
ensembl
updated 12 months ago by
Shreyash
• 0 • written 5.4 years ago by
rtwest
• 0
2
votes
4
replies
3.7k
views
How to convert large gene counts data into matrix?
R
Bioconductor
singlecell
bioinformatics
seurat
updated 9 weeks ago by
Gordon Smyth
50k • written 4.7 years ago by
sambunga094
• 0
1
vote
4
replies
1.4k
views
RNA-seq analysis using R
limma
rnaseq
convert
R
updated 12 months ago by
Gordon Smyth
50k • written 5.4 years ago by
justinkablan225
• 0
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
0
votes
3
replies
1.6k
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R
oligoClasses
Oligoclass
Bioconductor
Oligo
written 3.1 years ago by
tanya
• 0
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 14 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
0
votes
3
replies
458
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse
R
SingleCellExperiment
SingleCellData
updated 4 months ago by
daenerystargaryen56
• 0 • written 4 months ago by
Sitapriya
• 0
1
vote
3
replies
831
views
tximport error
tximport
r
updated 12 months ago by
Michael Love
41k • written 12 months ago by
Joana
• 0
1
vote
3
replies
1.8k
views
DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind
R
chipseq
updated 4 months ago by
Rory Stark
★ 5.1k • written 6.5 years ago by
kyliecode
• 0
3
votes
3
replies
4.5k
views
Genelist input for ClusterProfiler
R
ClusterProfiler
Enrichment
Pathway
updated 10 months ago by
Guido Hooiveld
★ 3.9k • written 4.0 years ago by
t.b.kuipers
• 0
1
vote
3
replies
1.3k
views
Error in the UcscTrack() in package "Gviz"
DMR
Methylation
R
Gviz
updated 5 months ago by
Robert Ivanek
▴ 730 • written 3.0 years ago by
ltzhou
• 0
0
votes
2
replies
531
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq
HTSeq
R
8 months ago • updated 7 months ago
yr542
• 0
0
votes
2
replies
1.2k
views
Trouble Loading Data into Champ
loaddata
ChAMPdata
champload
R
ChAMP
updated 10 months ago by
hfbarrerat
• 0 • written 3.1 years ago by
Bethan
• 0
0
votes
2
replies
2.0k
views
Creating a qPCRset object from a text file
qPCRset object
nondetects
r
package
txt
updated 6 months ago by
Nat.Nataren
• 0 • written 6.3 years ago by
s.m.may
• 0
1
vote
2
replies
577
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl
R
biomaRt
8 months ago
Miguel
• 0
0
votes
1
reply
484
views
DEseq2 Single cell data paired design
R
updated 11 months ago by
Marek Gierlinski
▴ 30 • written 11 months ago by
Caro
• 0
0
votes
1
reply
613
views
Subtype specific differential expression analysis
R
limmaGUI
edgeR
limma
regutools
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
qiz218591
• 0
0
votes
1
reply
1.4k
views
Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG
GAGE
NaN
R
DESeq2
updated 11 months ago by
Rob
• 0 • written 5.5 years ago by
owen.donohoe
• 0
0
votes
1
reply
501
views
Gene enrichment analysis
analysis
R
GOfuncR
updated 10 months ago by
Lluís Revilla Sancho
▴ 730 • written 10 months ago by
Eliza
• 0
0
votes
0
replies
104
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R
ATACseqQC
6 weeks ago
danalvoronov
▴ 10
0
votes
0
replies
206
views
multipollutant models
statistics
Regression
r
limma
4 months ago
Jitendra
▴ 10
36 results • Page
1 of 1
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Replies
Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
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.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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