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r
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17
votes
14
replies
39k
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LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq
differential gene expression
logfc
limma
R
updated 22 months ago by
OE
• 0 • written 6.7 years ago by
cms72
▴ 20
33
votes
16
replies
39k
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 2.1 years ago by
Hongwei
▴ 20 • written 7.3 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 6.0 years ago by
Merlin
▴ 10
0
votes
5
replies
24k
views
package DESeq2 installation with R.
deseq2
R
package installation
updated 2.9 years ago by
Michael Love
41k • written 6.1 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 5.4 years ago by
g.k
• 0
9
votes
8
replies
21k
views
Integrating DESeq2 and TopGO for Enrichment
go
deseq2
rnaseq
r
updated 9.2 years ago by
Bernd Klaus
▴ 610 • written 9.2 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
7.0 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 8.1 years ago by
Assa Yeroslaviz
★ 1.5k • written 8.1 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 7.5 years ago by
Mike Smith
★ 6.5k • written 7.5 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 20 months ago by
James W. MacDonald
65k • written 2.7 years ago by
onokaisaac
• 0
4
votes
1
reply
14k
views
The latest version of R is 3.5.1 and it is not compatible with many Bioconductor packages.
R
deseq
tcgabiolinks
5.7 years ago
ansari.sarabio
• 0
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
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 15 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
6
votes
2
replies
12k
views
DEseq2 - Use normalized DEseq2 counts to plot most expressed genes per group
deseq2
R
rnaseq
updated 8.3 years ago by
Michael Love
41k • written 8.3 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 4.4 years ago by
Kevin Blighe
★ 3.9k • written 4.4 years ago by
zeina.bourhane
• 0
1
vote
1
reply
11k
views
Pheatmap clustering and row annotation
R
pheatmap
cutree
6.6 years ago
meseretbrihanu
▴ 10
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
1
vote
1
reply
9.8k
views
Undertanding how DESeq2 handles multiple test conditions
rnaseq
deseq2
r
updated 9.2 years ago by
Ryan C. Thompson
★ 7.9k • written 9.2 years ago by
nw328
▴ 20
1
vote
6
replies
9.8k
views
Change fontsize/remove name of annotation ComplexHeatmap package
r
rnaseq
complexHeatmap
annotation
updated 3.8 years ago by
Zuguang Gu
▴ 260 • written 3.8 years ago by
camillab.
▴ 10
0
votes
5
replies
9.2k
views
tximport all(file.exists(files)) is not TRUE
bioconductor
tximport
rnaseq
R
updated 4 weeks ago by
Eva
• 0 • written 7.6 years ago by
ctl
• 0
0
votes
1
reply
9.2k
views
"No genes can be mapped...." using enrichGO in clusterProfiler
R
TAIR
clusterProfiler
enrichGO
Arabidopsis
updated 3.0 years ago by
Guido Hooiveld
★ 3.9k • written 3.0 years ago by
abby-s
• 0
4
votes
10
replies
9.1k
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
8.2 years ago • updated 7.8 years ago
pertille
• 0
1
vote
6
replies
8.9k
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
8.9k
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
8.8k
views
Extracting custom post-normalization counts from DESeq2
deseq2
r
ruvseq
normalization
rnaseq
8.8 years ago
nickp60
• 0
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
2
votes
1
reply
8.2k
views
Error: status was 'SSL connect error'
bioconductor
proxy
macOS
R
RStudio
updated 4.5 years ago by
Martin Morgan
25k • written 4.5 years ago by
mcall
▴ 20
2
votes
4
replies
7.9k
views
Deconvolution with CIBERSORT: input data
normalization
r
vst
cibersort
updated 3.7 years ago by
Kevin Blighe
★ 3.9k • written 3.7 years ago by
Matan G.
▴ 60
2
votes
2
replies
7.9k
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
0
votes
2
replies
7.7k
views
Add selected row names on pheatmap
R
pheatmap
updated 3.4 years ago by
ATpoint
★ 4.0k • written 3.4 years ago by
ecg1g15
▴ 20
2
votes
14
replies
7.5k
views
Calculating rpkm from counts data?
r
featurecounts
rpkm
tpm
edger
updated 14 months ago by
Chris
• 0 • written 6.7 years ago by
Biologist
▴ 110
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
6
votes
11
replies
7.3k
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
7.3k
views
WGCNA HELP - Error: REAL() can only be applied to a 'numeric', not a 'integer'
wgcna
rnaseq
R
bioconductor
updated 8.3 years ago by
Peter Langfelder
★ 3.0k • written 8.3 years ago by
sm15766
▴ 30
1
vote
2
replies
7.2k
views
Error in dyn.load(file, DLLpath = DLLpath, ...) :
R
qvalue
updated 8.0 years ago by
Martin Morgan
25k • written 8.0 years ago by
HS
▴ 10
1
vote
8
replies
7.0k
views
DESeq2: Continuous and discreate variables in the design
deseq2
R
rna-seq
design
updated 3.3 years ago by
Michael Love
41k • written 4.4 years ago by
raquelgarza95
• 0
6
votes
3
replies
6.9k
views
Heatmap Plotting in R
heatmap
R
bioconductor
8.7 years ago • updated 7.1 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
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
2
votes
2
replies
6.7k
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
2
votes
2
replies
6.7k
views
R 3.2.0 problem with DESeq2 - Hmisc error
deseq2
r
software error
updated 9.0 years ago by
Steve Lianoglou
★ 13k • written 9.0 years ago by
rclaire
▴ 20
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
5
votes
12
replies
6.4k
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
10
votes
10
replies
6.4k
views
biomaRt not working - lazy table error
error
lazy
R
biomaRt
table
updated 28 days ago by
juo5
• 0 • written 5 months ago by
Abhishek
▴ 10
3
votes
2
replies
6.2k
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 9.5 years ago by
James W. MacDonald
65k • written 9.5 years ago by
hmg
• 0
1
vote
2
replies
6.1k
views
How to convert Illumina HT_12_v4 annotation
convert
R
annotation
microarray
illumina human ht-12 v4
updated 16 months ago by
snijesh
▴ 20 • written 6.4 years ago by
p_donchev84
• 0
0
votes
2
replies
6.1k
views
Unable to install any bioconductor packages
R
biocinstaller
bioclite
package installation
6.7 years ago
sebastien200109
• 0
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Comment: How to make DGEList and design matrix by edgeR package
by
prity6459
• 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR
by
prity6459
• 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
It doesn't seem to me that there is necessarily any problem with the analysis. You that there are "too many low-reads" but actually there …
Answer: How to make DGEList and design matrix by edgeR package
by
Gordon Smyth
50k
Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…
Answer: Finding DEGs by using edgeR
by
Gordon Smyth
50k
I am not clear what you mean that you have already normalized your data. How exactly did you normalize the data? The best way to do an edg…
Votes
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
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