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3
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3
replies
13k
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How to fix 'long vectors not supported yet' error in R
r
updated 4 weeks ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
0
votes
0
replies
118
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R
ATACseqQC
9 weeks ago
danalvoronov
▴ 10
0
votes
4
replies
375
views
limma with interaction term
R
biostatistics
limma
Epigenetics
12 weeks ago • updated 10 weeks ago
Jitendra
▴ 10
0
votes
3
replies
1.6k
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R
oligoClasses
Oligoclass
Bioconductor
Oligo
written 3.2 years ago by
tanya
• 0
1
vote
5
replies
2.2k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo
microarray
r
bioconductor
written 9.2 years ago by
chandlerjd58
▴ 10
0
votes
3
replies
501
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 5 months ago by
Sitapriya
• 0
0
votes
0
replies
236
views
multipollutant models
statistics
Regression
r
limma
5 months ago
Jitendra
▴ 10
3
votes
4
replies
536
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
5 months ago
pl23
• 0
1
vote
3
replies
1.4k
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
10
replies
819
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R
BioMart
biomaRt
5 months ago • updated 9 weeks ago
ScafioRuo
• 0
10
votes
10
replies
7.0k
views
biomaRt not working - lazy table error
error
lazy
R
biomaRt
table
updated 6 weeks ago by
juo5
• 0 • written 6 months ago by
Abhishek
▴ 10
0
votes
2
replies
563
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq
HTSeq
R
9 months ago • updated 8 months ago
yr542
• 0
1
vote
2
replies
613
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl
R
biomaRt
9 months ago
Miguel
• 0
2
votes
5
replies
1.4k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R
edgeR
RNASeq
9 months ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
523
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
2
replies
1.2k
views
Trouble Loading Data into Champ
loaddata
ChAMPdata
champload
R
ChAMP
updated 11 months ago by
hfbarrerat
• 0 • written 3.2 years ago by
Bethan
• 0
4
votes
8
replies
2.2k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2
limma
Normalization
R
updated 11 months ago by
Gordon Smyth
50k • written 17 months ago by
Sabiha
▴ 20
4
votes
5
replies
1.9k
views
time course microarray data ArrayExpress database
R
GillespieColin
ArrayExpress
import
TimeSeriesExperiment
updated 7 months ago by
jacorvar
▴ 40 • written 19 months ago by
eraldagjika
▴ 20
4
votes
7
replies
14k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 7 months ago by
Gordon Smyth
50k • written 22 months ago by
Mohamed
▴ 30
7
votes
5
replies
7.0k
views
biomaRt server error, and mirrors do not help
ensembl
biomaRt
R
updated 6 months ago by
Ke
• 0 • written 2.0 years ago by
kieran.short
▴ 40
22
votes
15
replies
7.5k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt
RNASeqData
R
updated 6 months ago by
Marie
▴ 10 • written 2.1 years ago by
Dina
▴ 50
1
vote
12
replies
2.4k
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 3 months ago by
Mary
• 0 • written 2.5 years ago by
Ming
▴ 380
3
votes
3
replies
4.7k
views
Genelist input for ClusterProfiler
R
ClusterProfiler
Enrichment
Pathway
updated 11 months ago by
Guido Hooiveld
★ 3.9k • written 4.0 years ago by
t.b.kuipers
• 0
2
votes
4
replies
3.8k
views
How to convert large gene counts data into matrix?
R
Bioconductor
singlecell
bioinformatics
seurat
updated 12 weeks ago by
Gordon Smyth
50k • written 4.8 years ago by
sambunga094
• 0
0
votes
1
reply
1.4k
views
Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG
GAGE
NaN
R
DESeq2
updated 12 months ago by
Rob
• 0 • written 5.5 years ago by
owen.donohoe
• 0
0
votes
2
replies
2.1k
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
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
★ 5.2k • written 6.6 years ago by
kyliecode
• 0
0
votes
6
replies
8.7k
views
No gene can be mapped error with clusterprofiler
clusterprofiler
r
updated 4 months ago by
Guido Hooiveld
★ 3.9k • written 7.3 years ago by
prp291
• 0
0
votes
5
replies
9.3k
views
tximport all(file.exists(files)) is not TRUE
bioconductor
tximport
rnaseq
R
updated 7 weeks ago by
Eva
• 0 • written 7.6 years ago by
ctl
• 0
29 results • Page
1 of 1
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Replies
Comment: Help with running egsea()
by
Chris
• 0
I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
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