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r
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17
votes
14
replies
39k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq
differential gene expression
logfc
limma
R
updated 21 months ago by
OE
• 0 • written 6.7 years ago by
cms72
▴ 20
33
votes
16
replies
38k
views
Differential expression analysis starting from TPM data
R
TPM
updated 6.7 years ago by
Gordon Smyth
50k • written 6.7 years ago by
cahidora
▴ 90
24
votes
6
replies
38k
views
DESeq2: Is it possible to convert read counts to expression values via TPM and return these values?
deseq2
r
updated 24 months ago by
Hongwei
▴ 20 • written 7.2 years ago by
tombernardryan
▴ 50
1
vote
19
replies
25k
views
Import bamfiles for RNAsequencing analysis
R
rnaseq
bam file
updated 5.9 years ago by
Gordon Smyth
50k • written 5.9 years ago by
Merlin
▴ 10
0
votes
5
replies
24k
views
package DESeq2 installation with R.
deseq2
R
package installation
updated 2.8 years ago by
Michael Love
41k • written 6.0 years ago by
layeb
• 0
4
votes
3
replies
22k
views
Fisher test in Rna seq
rna-seq
rnaseq
r
updated 4.7 years ago by
Gordon Smyth
50k • written 5.3 years ago by
g.k
• 0
9
votes
8
replies
21k
views
Integrating DESeq2 and TopGO for Enrichment
go
deseq2
rnaseq
r
updated 9.1 years ago by
Bernd Klaus
▴ 610 • written 9.1 years ago by
nw328
▴ 20
0
votes
4
replies
21k
views
DESeq2: How do I compare certain samples that are in two groups and two treatments
deseq2
rnaseq
R
6.9 years ago
zeynep.nenseth
• 0
2
votes
10
replies
20k
views
Heatmap with error message: `x' must be a numeric matrix
r
heatmap
numericmatrix
updated 8.0 years ago by
Assa Yeroslaviz
★ 1.5k • written 8.0 years ago by
Biologist
▴ 110
2
votes
9
replies
19k
views
Error in file(con, “r”) : cannot open the connection
r
phyloseq
import_biom
otu
qiime
updated 8.5 years ago by
mcmurdie
▴ 20 • written 8.5 years ago by
moanam
• 0
3
votes
5
replies
17k
views
Any quick solution for fixing error : "$ operator is invalid for atomic vectors" ?
r
granges
dplyr
error handling
updated 7.4 years ago by
Mike Smith
★ 6.5k • written 7.4 years ago by
Jurat Shahidin
▴ 80
0
votes
4
replies
14k
views
hclust(d, method = method) : NA/NaN/Inf in foreign function call (arg 10)
R
pheatmap
xcms
updated 19 months ago by
James W. MacDonald
65k • written 2.6 years ago by
onokaisaac
• 0
4
votes
1
reply
13k
views
The latest version of R is 3.5.1 and it is not compatible with many Bioconductor packages.
R
deseq
tcgabiolinks
5.6 years ago
ansari.sarabio
• 0
3
votes
1
reply
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 5.1 years ago by
Mike Smith
★ 6.5k • written 5.1 years ago by
r.tor
• 0
4
votes
7
replies
13k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 6 months ago by
Gordon Smyth
50k • written 21 months ago by
Mohamed
▴ 30
6
votes
2
replies
12k
views
DEseq2 - Use normalized DEseq2 counts to plot most expressed genes per group
deseq2
R
rnaseq
updated 8.2 years ago by
Michael Love
41k • written 8.2 years ago by
Bstn132
• 0
2
votes
5
replies
11k
views
Calculating FPKM from raw counts data using fpkm() in deseq2
deseq2
r
fpkm()
geneexpression
updated 5.5 years ago by
Michael Love
41k • written 5.5 years ago by
Beginner
▴ 60
1
vote
1
reply
11k
views
Install Bioconductor in R studio
R
updated 4.3 years ago by
Kevin Blighe
★ 3.9k • written 4.3 years ago by
zeina.bourhane
• 0
1
vote
1
reply
11k
views
Pheatmap clustering and row annotation
R
pheatmap
cutree
6.5 years ago
meseretbrihanu
▴ 10
8
votes
11
replies
10k
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
1
vote
1
reply
9.8k
views
Undertanding how DESeq2 handles multiple test conditions
rnaseq
deseq2
r
updated 9.1 years ago by
Ryan C. Thompson
★ 7.9k • written 9.1 years ago by
nw328
▴ 20
1
vote
6
replies
9.6k
views
Change fontsize/remove name of annotation ComplexHeatmap package
r
rnaseq
complexHeatmap
annotation
updated 3.8 years ago by
Zuguang Gu
▴ 240 • written 3.8 years ago by
camillab.
▴ 10
0
votes
5
replies
9.1k
views
tximport all(file.exists(files)) is not TRUE
bioconductor
tximport
rnaseq
R
updated 8 days ago by
Eva
• 0 • written 7.5 years ago by
ctl
• 0
0
votes
1
reply
9.0k
views
"No genes can be mapped...." using enrichGO in clusterProfiler
R
TAIR
clusterProfiler
enrichGO
Arabidopsis
updated 2.9 years ago by
Guido Hooiveld
★ 3.9k • written 2.9 years ago by
abby-s
• 0
4
votes
10
replies
9.0k
views
How can I extract sequences from a FASTA file for each of the intervals defined in a BED file using R?
R
bioconductor
granges
8.1 years ago • updated 7.7 years ago
pertille
• 0
1
vote
6
replies
8.8k
views
Getting HGNC gene names from Ensembl transcript IDs (e.g., ENST0000...)
rnaseq
r
biomart
updated 8.4 years ago by
Johannes Rainer
★ 2.0k • written 8.4 years ago by
kmuench
▴ 40
2
votes
10
replies
8.7k
views
adjusted p-values and p-values problems!
pvalue
adjusted pvalue
r
bonferroni
rna-seq
updated 7.5 years ago by
Michael Love
41k • written 7.5 years ago by
fromhj304
▴ 10
4
votes
14
replies
8.7k
views
Extracting custom post-normalization counts from DESeq2
deseq2
r
ruvseq
normalization
rnaseq
8.7 years ago
nickp60
• 0
0
votes
6
replies
8.6k
views
No gene can be mapped error with clusterprofiler
clusterprofiler
r
updated 11 weeks ago by
Guido Hooiveld
★ 3.9k • written 7.2 years ago by
prp291
• 0
2
votes
1
reply
8.1k
views
Error: status was 'SSL connect error'
bioconductor
proxy
macOS
R
RStudio
updated 4.4 years ago by
Martin Morgan
25k • written 4.4 years ago by
mcall
▴ 20
2
votes
2
replies
7.8k
views
Convert Expression Set into a Matrix or Data Frame
microarray
biobase
affy
R
updated 8.2 years ago by
Diego Diez
▴ 760 • written 8.2 years ago by
hshabbeer.09
• 0
2
votes
4
replies
7.7k
views
Deconvolution with CIBERSORT: input data
normalization
r
vst
cibersort
updated 3.6 years ago by
Kevin Blighe
★ 3.9k • written 3.6 years ago by
Matan G.
▴ 50
0
votes
2
replies
7.5k
views
Add selected row names on pheatmap
R
pheatmap
updated 3.3 years ago by
ATpoint
★ 4.0k • written 3.3 years ago by
ecg1g15
▴ 20
2
votes
14
replies
7.4k
views
Calculating rpkm from counts data?
r
featurecounts
rpkm
tpm
edger
updated 13 months ago by
Chris
• 0 • written 6.6 years ago by
Biologist
▴ 110
6
votes
11
replies
7.2k
views
How do I split GRange object (set of genomic ranges with 2 metadata column) by chromosome?
granges
split
r
updated 2.3 years ago by
jon.klonowski
▴ 40 • written 8.2 years ago by
Jurat Shahidin
▴ 80
3
votes
5
replies
7.2k
views
WGCNA HELP - Error: REAL() can only be applied to a 'numeric', not a 'integer'
wgcna
rnaseq
R
bioconductor
updated 8.2 years ago by
Peter Langfelder
★ 2.9k • written 8.2 years ago by
sm15766
▴ 30
22
votes
15
replies
7.2k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt
RNASeqData
R
updated 4 months ago by
Marie
▴ 10 • written 23 months ago by
Dina
▴ 50
1
vote
2
replies
7.1k
views
Error in dyn.load(file, DLLpath = DLLpath, ...) :
R
qvalue
updated 7.9 years ago by
Martin Morgan
25k • written 7.9 years ago by
HS
▴ 10
6
votes
3
replies
6.9k
views
Heatmap Plotting in R
heatmap
R
bioconductor
8.7 years ago • updated 7.0 years ago
Deepak Tanwar
▴ 10
4
votes
8
replies
6.9k
views
getGEO - cannot Open URL issue
getGEO
R
GEOquery
8.5 years ago
alptaciroglu
▴ 50
1
vote
8
replies
6.9k
views
DESeq2: Continuous and discreate variables in the design
deseq2
R
rna-seq
design
updated 3.2 years ago by
Michael Love
41k • written 4.3 years ago by
raquelgarza95
• 0
2
votes
2
replies
6.6k
views
R 3.2.0 problem with DESeq2 - Hmisc error
deseq2
r
software error
updated 8.9 years ago by
Steve Lianoglou
★ 13k • written 8.9 years ago by
rclaire
▴ 20
2
votes
2
replies
6.6k
views
Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression
GeneExpression
DESeq2
R
updated 2.5 years ago by
ATpoint
★ 4.0k • written 2.5 years ago by
janjoy
▴ 10
0
votes
6
replies
6.6k
views
Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData
deseq2
R
genomics
6.2 years ago
mokunf
• 0
7
votes
5
replies
6.6k
views
biomaRt server error, and mirrors do not help
ensembl
biomaRt
R
updated 5 months ago by
Ke
• 0 • written 23 months ago by
kieran.short
▴ 40
5
votes
12
replies
6.3k
views
Filtering step for differential analysis in edgeR
r
edger
differential gene expression
filtering
bioconductor
updated 5.9 years ago by
Gordon Smyth
50k • written 5.9 years ago by
Biologist
▴ 110
3
votes
2
replies
6.1k
views
Trying to understand differential gene expression through Venn Diagrams from the 'limma' R package: why is there a number outside my diagram?
limma
r
venn diagram
differential expression
updated 9.4 years ago by
James W. MacDonald
65k • written 9.4 years ago by
hmg
• 0
0
votes
2
replies
6.1k
views
Unable to install any bioconductor packages
R
biocinstaller
bioclite
package installation
6.6 years ago
sebastien200109
• 0
1
vote
2
replies
6.0k
views
How to convert Illumina HT_12_v4 annotation
convert
R
annotation
microarray
illumina human ht-12 v4
updated 15 months ago by
snijesh
▴ 20 • written 6.3 years ago by
p_donchev84
• 0
3
votes
4
replies
6.0k
views
Subset GRanges object into new object
R
genomicranges
subsetting
6.4 years ago
jhanks1981
• 0
50 results • Page
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Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
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50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
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by
Gordon Smyth
50k
I already know that you using CEL files because you need them to perform RMA normalization. Yes, you should follow the advice I have alread…
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DESeq2 normalization vs VST vs rlog
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