Showing : r • reset
33
votes
16
replies
35k
views
Differential expression analysis starting from TPM data
R TPM
updated 6.2 years ago by 48k • written 6.2 years ago by ▴ 90
16
votes
14
replies
35k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq differential gene expression logfc limma R
updated 15 months ago by • 0 • written 6.2 years ago by ▴ 20
24
votes
6
replies
34k
views
DESeq2: Is it possible to convert read counts to expression values via TPM and return these values?
deseq2 r
updated 18 months ago by ▴ 20 • written 6.7 years ago by ▴ 50
0
votes
5
replies
23k
views
package DESeq2 installation with R.
deseq2 R package installation
updated 2.3 years ago by 40k • written 5.5 years ago by • 0
1
vote
19
replies
23k
views
Import bamfiles for RNAsequencing analysis
R rnaseq bam file
updated 5.4 years ago by 48k • written 5.4 years ago by ▴ 10
4
votes
3
replies
20k
views
Fisher test in Rna seq
rna-seq rnaseq r
updated 4.2 years ago by 48k • written 4.8 years ago by • 0
9
votes
8
replies
20k
views
Integrating DESeq2 and TopGO for Enrichment
go deseq2 rnaseq r
updated 8.6 years ago by ▴ 610 • written 8.6 years ago by ▴ 20
2
votes
10
replies
20k
views
Heatmap with error message: `x' must be a numeric matrix
r heatmap numericmatrix
updated 7.5 years ago by ★ 1.5k • written 7.5 years ago by ▴ 110
0
votes
4
replies
19k
views
DESeq2: How do I compare certain samples that are in two groups and two treatments
deseq2 rnaseq R
6.4 years ago zeynep.nenseth • 0
2
votes
9
replies
19k
views
Error in file(con, “r”) : cannot open the connection
r phyloseq import_biom otu qiime
updated 8.0 years ago by ▴ 20 • written 8.0 years ago by • 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 7.0 years ago by ★ 6.1k • written 7.0 years ago by ▴ 80
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
5.1 years ago ansari.sarabio • 0
6
votes
2
replies
12k
views
DEseq2 - Use normalized DEseq2 counts to plot most expressed genes per group
deseq2 R rnaseq
updated 7.7 years ago by 40k • written 7.7 years ago by • 0
3
votes
1
reply
11k
views
How to fix 'long vectors not supported yet' error in R
r
updated 4.6 years ago by ★ 6.1k • written 4.6 years ago by • 0
0
votes
4
replies
11k
views
hclust(d, method = method) : NA/NaN/Inf in foreign function call (arg 10)
R pheatmap xcms
updated 13 months ago by 63k • written 2.1 years ago by • 0
1
vote
1
reply
10k
views
Pheatmap clustering and row annotation
R pheatmap cutree
6.0 years ago meseretbrihanu ▴ 10
1
vote
5
replies
9.7k
views
Calculating FPKM from raw counts data using fpkm() in deseq2
deseq2 r fpkm() geneexpression
updated 5.0 years ago by 40k • written 5.0 years ago by ▴ 50
8
votes
11
replies
9.7k
views
R: error while reading .h5 files from R using rdhf5 package
rhdf5 r hdf5
updated 5 months ago by • 0 • written 6.3 years ago by ▴ 10
1
vote
1
reply
9.6k
views
Undertanding how DESeq2 handles multiple test conditions
rnaseq deseq2 r
updated 8.6 years ago by 7.8k • written 8.6 years ago by ▴ 20
1
vote
1
reply
9.4k
views
Install Bioconductor in R studio
R
updated 3.8 years ago by 3.8k • written 3.8 years ago by • 0
4
votes
10
replies
8.6k
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
7.6 years ago • updated 7.2 years ago pertille • 0
1
vote
6
replies
8.4k
views
Getting HGNC gene names from Ensembl transcript IDs (e.g., ENST0000...)
rnaseq r biomart
updated 7.9 years ago by ★ 2.0k • written 7.9 years ago by ▴ 40
2
votes
7
replies
8.3k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 14 days ago by 48k • written 15 months ago by ▴ 20
4
votes
14
replies
8.3k
views
Extracting custom post-normalization counts from DESeq2
deseq2 r ruvseq normalization rnaseq
8.2 years ago nickp60 • 0
0
votes
4
replies
8.2k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
7.0 years ago ctl • 0
1
vote
6
replies
8.1k
views
Change fontsize/remove name of annotation ComplexHeatmap package
r rnaseq complexHeatmap annotation
updated 3.3 years ago by ▴ 240 • written 3.3 years ago by ▴ 10
0
votes
1
reply
8.0k
views
"No genes can be mapped...." using enrichGO in clusterProfiler
R TAIR clusterProfiler enrichGO Arabidopsis
updated 2.4 years ago by ★ 3.7k • written 2.4 years ago by • 0
2
votes
10
replies
8.0k
views
adjusted p-values and p-values problems!
pvalue adjusted pvalue r bonferroni rna-seq
updated 7.0 years ago by 40k • written 7.0 years ago by ▴ 10
0
votes
5
replies
7.9k
views
No gene can be mapped error with clusterprofiler
clusterprofiler r
updated 6.7 years ago by ★ 1.2k • written 6.7 years ago by • 0
2
votes
2
replies
7.3k
views
Convert Expression Set into a Matrix or Data Frame
microarray biobase affy R
updated 7.7 years ago by ▴ 760 • written 7.7 years ago by • 0
3
votes
5
replies
6.9k
views
WGCNA HELP - Error: REAL() can only be applied to a 'numeric', not a 'integer'
wgcna rnaseq R bioconductor
updated 7.7 years ago by ★ 2.8k • written 7.7 years ago by ▴ 30
6
votes
3
replies
6.7k
views
Heatmap Plotting in R
heatmap R bioconductor
8.2 years ago • updated 6.5 years ago Deepak Tanwar ▴ 10
1
vote
2
replies
6.7k
views
Error in dyn.load(file, DLLpath = DLLpath, ...) :
R qvalue
updated 7.4 years ago by 25k • written 7.4 years ago by ▴ 10
6
votes
11
replies
6.7k
views
How do I split GRange object (set of genomic ranges with 2 metadata column) by chromosome?
granges split r
updated 21 months ago by ▴ 40 • written 7.7 years ago by ▴ 80
2
votes
14
replies
6.6k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 7 months ago by • 0 • written 6.1 years ago by ▴ 110
2
votes
4
replies
6.6k
views
Deconvolution with CIBERSORT: input data
normalization r vst cibersort
updated 3.1 years ago by 3.8k • written 3.1 years ago by ▴ 50
4
votes
8
replies
6.5k
views
getGEO - cannot Open URL issue
getGEO R GEOquery
8.0 years ago alptaciroglu ▴ 50
2
votes
2
replies
6.4k
views
R 3.2.0 problem with DESeq2 - Hmisc error
deseq2 r software error
updated 8.4 years ago by 13k • written 8.4 years ago by ▴ 20
2
votes
1
reply
6.4k
views
Error: status was 'SSL connect error'
bioconductor proxy macOS R RStudio
updated 3.9 years ago by 25k • written 3.9 years ago by ▴ 20
0
votes
2
replies
6.3k
views
Add selected row names on pheatmap
R pheatmap
updated 2.8 years ago by ★ 3.4k • written 2.8 years ago by ▴ 20
0
votes
6
replies
6.1k
views
Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData
deseq2 R genomics
5.7 years ago mokunf • 0
0
votes
2
replies
5.9k
views
Unable to install any bioconductor packages
R biocinstaller bioclite package installation
6.1 years ago sebastien200109 • 0
3
votes
2
replies
5.8k
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 8.9 years ago by 63k • written 8.9 years ago by • 0
22
votes
14
replies
5.8k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 16 months ago by • 0 • written 17 months ago by ▴ 50
8
votes
9
replies
5.6k
views
could not find symbol "keepNA" in environment of the generic function
R function genomicalignments genomicranges summarizeoverlaps
updated 8.2 years ago by • 0 • written 8.2 years ago by ★ 1.5k
4
votes
12
replies
5.6k
views
Filtering step for differential analysis in edgeR
r edger differential gene expression filtering bioconductor
updated 5.4 years ago by 48k • written 5.4 years ago by ▴ 110
1
vote
8
replies
5.6k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 2.7 years ago by 40k • written 3.8 years ago by • 0
0
votes
1
reply
5.5k
views
Subset data within DeSeq results object
deseq2 R rna-seq
updated 6.1 years ago by 40k • written 6.1 years ago by • 0
2
votes
2
replies
5.4k
views
Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression GeneExpression DESeq2 R
updated 24 months ago by ★ 3.4k • written 24 months ago by ▴ 10
3
votes
4
replies
5.3k
views
Subset GRanges object into new object
R genomicranges subsetting
5.9 years ago jhanks1981 • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Michael Love 40k
Did you manually calculate RPMs? Try `fpm(dds)` for comparison, as this also uses DESeq2 median ratio scaling.
Comment: collapseReplicates error after tximeta by Michael Love 40k
A note: I've now changed collapseReplicates() to output a loud warning when it is run on a DESeqDataSet (SummarizedExperiment) with more th…
Comment: Suggested package missing from Development version of Bioconductor by shepherl 3.5k
Have you tried reaching out to the maintainers? If they do not fix the package it will remain unavailable and cause ERROR in your package.…
Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …
Votes
Comment: Batch correction and repeated measures
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
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