Showing : r • reset
26
votes
16
replies
27k
views
Differential expression analysis starting from TPM data
R TPM
updated 5.0 years ago by 46k • written 5.0 years ago by ▴ 60
23
votes
6
replies
26k
views
DESeq2: Is it possible to convert read counts to expression values via TPM and return these values?
deseq2 r
updated 4 months ago by ▴ 20 • written 5.6 years ago by ▴ 50
14
votes
14
replies
23k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq differential gene expression logfc limma R
updated 7 weeks ago by • 0 • written 5.1 years ago by ▴ 20
2
votes
10
replies
18k
views
Heatmap with error message: `x' must be a numeric matrix
r heatmap numericmatrix
updated 6.4 years ago by ★ 1.5k • written 6.4 years ago by ▴ 90
0
votes
5
replies
18k
views
package DESeq2 installation with R.
deseq2 R package installation
updated 14 months ago by 37k • written 4.4 years ago by • 0
2
votes
9
replies
17k
views
Error in file(con, “r”) : cannot open the connection
r phyloseq import_biom otu qiime
updated 6.8 years ago by ▴ 20 • written 6.8 years ago by • 0
8
votes
8
replies
17k
views
Integrating DESeq2 and TopGO for Enrichment
go deseq2 rnaseq r
updated 7.5 years ago by ▴ 600 • written 7.5 years ago by ▴ 20
3
votes
5
replies
16k
views
Any quick solution for fixing error : "$ operator is invalid for atomic vectors" ?
r granges dplyr error handling
updated 5.8 years ago by ★ 5.7k • written 5.8 years ago by ▴ 70
1
vote
19
replies
15k
views
Import bamfiles for RNAsequencing analysis
R rnaseq bam file
updated 4.3 years ago by 46k • written 4.3 years ago by ▴ 10
4
votes
3
replies
14k
views
Fisher test in Rna seq
rna-seq rnaseq r
updated 3.1 years ago by 46k • written 3.7 years ago by • 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
4.0 years ago ansari.sarabio • 0
0
votes
4
replies
13k
views
DESeq2: How do I compare certain samples that are in two groups and two treatments
deseq2 rnaseq R
5.3 years ago zeynep.nenseth • 0
4
votes
2
replies
10k
views
DEseq2 - Use normalized DEseq2 counts to plot most expressed genes per group
deseq2 R rnaseq
updated 6.6 years ago by 37k • written 6.6 years ago by • 0
1
vote
1
reply
9.2k
views
Undertanding how DESeq2 handles multiple test conditions
rnaseq deseq2 r
updated 7.5 years ago by 7.8k • written 7.5 years ago by ▴ 20
1
vote
1
reply
8.6k
views
Pheatmap clustering and row annotation
R pheatmap cutree
4.9 years ago meseretbrihanu ▴ 10
3
votes
1
reply
7.9k
views
How to fix 'long vectors not supported yet' error in R
r
updated 3.5 years ago by ★ 5.7k • written 3.5 years ago by • 0
4
votes
14
replies
7.7k
views
Extracting custom post-normalization counts from DESeq2
deseq2 r ruvseq normalization rnaseq
7.1 years ago nickp60 • 0
4
votes
10
replies
7.5k
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
6.5 years ago • updated 6.1 years ago pertille • 0
7
votes
10
replies
7.3k
views
R: error while reading .h5 files from R using rdhf5 package
rhdf5 r hdf5
updated 5.1 years ago by 13k • written 5.2 years ago by • 0
1
vote
6
replies
7.0k
views
Getting HGNC gene names from Ensembl transcript IDs (e.g., ENST0000...)
rnaseq r biomart
updated 6.7 years ago by ★ 2.0k • written 6.7 years ago by ▴ 40
2
votes
10
replies
6.3k
views
adjusted p-values and p-values problems!
pvalue adjusted pvalue r bonferroni rna-seq
updated 5.9 years ago by 37k • written 5.9 years ago by ▴ 10
6
votes
3
replies
6.3k
views
Heatmap Plotting in R
heatmap R bioconductor
7.1 years ago • updated 5.4 years ago Deepak Tanwar ▴ 10
2
votes
2
replies
6.2k
views
Convert Expression Set into a Matrix or Data Frame
microarray biobase affy R
updated 6.6 years ago by ▴ 760 • written 6.6 years ago by • 0
1
vote
5
replies
6.2k
views
Calculating FPKM from raw counts data using fpkm() in deseq2
deseq2 r fpkm() geneexpression
updated 3.9 years ago by 37k • written 3.9 years ago by ▴ 50
0
votes
4
replies
6.1k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
5.9 years ago ctl • 0
2
votes
2
replies
6.0k
views
R 3.2.0 problem with DESeq2 - Hmisc error
deseq2 r software error
updated 7.3 years ago by 13k • written 7.3 years ago by ▴ 20
3
votes
5
replies
5.9k
views
WGCNA HELP - Error: REAL() can only be applied to a 'numeric', not a 'integer'
wgcna rnaseq R bioconductor
updated 6.6 years ago by ★ 2.7k • written 6.6 years ago by ▴ 30
0
votes
5
replies
5.6k
views
No gene can be mapped error with clusterprofiler
clusterprofiler r
updated 5.6 years ago by ★ 1.2k • written 5.6 years ago by • 0
4
votes
8
replies
5.5k
views
getGEO - cannot Open URL issue
getGEO R GEOquery
6.8 years ago alptaciroglu ▴ 50
0
votes
2
replies
5.5k
views
Unable to install any bioconductor packages
R biocinstaller bioclite package installation
5.0 years ago sebastien200109 • 0
6
votes
11
replies
5.4k
views
How do I split GRange object (set of genomic ranges with 2 metadata column) by chromosome?
granges split r
updated 8 months ago by ▴ 40 • written 6.5 years ago by ▴ 70
1
vote
1
reply
5.4k
views
Install Bioconductor in R studio
R
updated 2.7 years ago by 3.6k • written 2.7 years ago by • 0
8
votes
9
replies
5.1k
views
could not find symbol "keepNA" in environment of the generic function
R function genomicalignments genomicranges summarizeoverlaps
updated 7.1 years ago by • 0 • written 7.1 years ago by ★ 1.5k
3
votes
2
replies
5.1k
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 7.8 years ago by 60k • written 7.8 years ago by • 0
1
vote
2
replies
5.0k
views
Error in dyn.load(file, DLLpath = DLLpath, ...) :
R qvalue
updated 6.3 years ago by 25k • written 6.3 years ago by ▴ 10
2
votes
13
replies
4.9k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 5.0 years ago by ▴ 20 • written 5.0 years ago by ▴ 90
0
votes
6
replies
4.8k
views
Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData
deseq2 R genomics
4.5 years ago mokunf • 0
1
vote
2
replies
4.5k
views
explanation of makeContrasts function of limma package
limma microarray R geneexpression
updated 7.0 years ago by ★ 27k • written 7.0 years ago by ▴ 10
0
votes
1
reply
4.4k
views
Subset data within DeSeq results object
deseq2 R rna-seq
updated 5.0 years ago by 37k • written 5.0 years ago by • 0
5
votes
22
replies
4.3k
views
sqliteSendQuery error in AnnotationForge bioconductor package
bioconductor annotationforge annotationdbi annotation r
updated 6.1 years ago by ▴ 990 • written 7.5 years ago by • 0
3
votes
5
replies
4.2k
views
SingleCellExperiment function in SingleCellExperiment package returns error (when reproducing example)
R bioconductor singlecellexperiment single cell
updated 4.8 years ago by • 0 • written 4.8 years ago by ▴ 10
4
votes
12
replies
4.1k
views
Filtering step for differential analysis in edgeR
r edger differential gene expression filtering bioconductor
updated 4.3 years ago by 46k • written 4.3 years ago by ▴ 90
1
vote
4
replies
3.9k
views
do.call error "second argument must be a list" with GRanges object [closed]
r error handling
5.5 years ago Jurat Shahidin ▴ 70
6
votes
10
replies
3.9k
views
defining a function for multiple paired t.test in many rows of a microarray dataset
microarray r t.test bioconductor
updated 7.6 years ago by 46k • written 7.6 years ago by ▴ 800
1
vote
6
replies
3.9k
views
Change fontsize/remove name of annotation ComplexHeatmap package
r rnaseq complexHeatmap annotation
updated 2.2 years ago by ▴ 220 • written 2.2 years ago by ▴ 10
1
vote
1
reply
3.9k
views
MA plot in R
rstudio r plotMA
5.2 years ago g.k • 0
3
votes
6
replies
3.8k
views
Principle component analysis plot with gene expression data
r pca rnaseq edger ggbiplot
updated 4.3 years ago by 60k • written 4.3 years ago by ▴ 90
1
vote
3
replies
3.7k
views
Error in cleanContrast
deseq2 r error
updated 5.7 years ago by 37k • written 5.7 years ago by • 0
4
votes
3
replies
3.6k
views
Splitting a GRanges object into List of GRange objects by position.
R granges subsett grangeslist group
updated 5.5 years ago by ★ 5.7k • written 5.5 years ago by ▴ 50
1
vote
8
replies
3.6k
views
Cannot read Biom file
r biomformat phyloseq
updated 4.8 years ago by ▴ 990 • written 4.8 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: errors in annotation by Josie • 0
OK thanks James. I'll send off an email to GenBank, see if they feel inclined to correct some errors.
Answer: Conversion of UniProt to Ensembl by James W. MacDonald 60k
I will provide an example below. But first, there is a vignette for biomaRt (actually two), and it has extensive examples of how to use the…
Comment: the difference between getGEO and getGEOSuppFiles by Fatemeh • 0
thank you!
Answer: the difference between getGEO and getGEOSuppFiles by James W. MacDonald 60k
When submitting data to GEO, you are supposed to provide both the raw data and a matrix of processed data. When you use `getGEO` you get th…
Comment: error running UniProt.ws by James W. MacDonald 60k
https://www.bioconductor.org/checkResults/3.15/bioc-LATEST/UniProt.ws/nebbiolo1-install.html
Votes
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
Answer: the difference between getGEO and getGEOSuppFiles
Answer: the difference between getGEO and getGEOSuppFiles
Answer: TPM normalization starting with read counts
Awards • All
Scholar to James W. MacDonald 60k
Popular Question to Matthew Ritchie ▴ 1000
Scholar to Thomas Carroll ▴ 410
Popular Question to rbenel ▴ 20
Popular Question to Gordon Smyth 46k
Locations • All
WEHI, Melbourne, Australia, just now
Canada, 3 minutes ago
United States, 9 minutes ago
United States, 11 minutes ago
Iraq, 13 minutes ago
Traffic: 292 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6