Showing : r • reset
22
votes
15
replies
7.3k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 5 months ago by ▴ 10 • written 2.0 years ago by ▴ 50
1
vote
12
replies
2.3k
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 12 weeks ago by • 0 • written 2.5 years ago by ▴ 380
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 • 0 • written 6.8 years ago by ▴ 10
10
votes
10
replies
6.3k
views
biomaRt not working - lazy table error
error lazy R biomaRt table
updated 27 days ago by • 0 • written 5 months ago by ▴ 10
0
votes
10
replies
782
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R BioMart biomaRt
5 months ago • updated 6 weeks ago ScafioRuo • 0
4
votes
8
replies
2.1k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 10 months ago by 50k • written 16 months ago by ▴ 20
4
votes
7
replies
13k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 7 months ago by 50k • written 21 months ago by ▴ 30
0
votes
6
replies
8.6k
views
No gene can be mapped error with clusterprofiler
clusterprofiler r
updated 3 months ago by ★ 3.9k • written 7.3 years ago by • 0
4
votes
5
replies
1.9k
views
time course microarray data ArrayExpress database
R GillespieColin ArrayExpress import TimeSeriesExperiment
updated 6 months ago by ▴ 40 • written 18 months ago by ▴ 20
0
votes
5
replies
9.2k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 29 days ago by • 0 • written 7.6 years ago by • 0
1
vote
5
replies
2.1k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 9.2 years ago by ▴ 10
2
votes
5
replies
1.3k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
9 months ago • updated 8 months ago mohammedtoufiq91 ▴ 10
7
votes
5
replies
6.8k
views
biomaRt server error, and mirrors do not help
ensembl biomaRt R
updated 6 months ago by • 0 • written 23 months ago by ▴ 40
0
votes
4
replies
865
views
Combine RNA-seq
BatchEffect R rnaseq
updated 11 months ago by ★ 1.3k • written 11 months ago by • 0
0
votes
4
replies
323
views
limma with interaction term
R biostatistics limma Epigenetics
9 weeks ago • updated 7 weeks ago Jitendra ▴ 10
2
votes
4
replies
1.6k
views
make TxDb from list of genes
R maketxdbfrombiomart maketxdbfromgranges rstudio ensembl
updated 12 months ago by • 0 • written 5.4 years ago by • 0
2
votes
4
replies
3.7k
views
How to convert large gene counts data into matrix?
R Bioconductor singlecell bioinformatics seurat
updated 9 weeks ago by 50k • written 4.7 years ago by • 0
1
vote
4
replies
1.4k
views
RNA-seq analysis using R
limma rnaseq convert R
updated 12 months ago by 50k • written 5.4 years ago by • 0
3
votes
4
replies
510
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
4 months ago pl23 • 0
0
votes
3
replies
1.6k
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R oligoClasses Oligoclass Bioconductor Oligo
written 3.1 years ago by • 0
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 14 days ago by • 0 • written 5.2 years ago by • 0
0
votes
3
replies
458
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 • 0 • written 4 months ago by • 0
1
vote
3
replies
831
views
tximport error
tximport r
updated 12 months ago by 41k • written 12 months ago by • 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 ★ 5.1k • written 6.5 years ago by • 0
3
votes
3
replies
4.5k
views
Genelist input for ClusterProfiler
R ClusterProfiler Enrichment Pathway
updated 10 months ago by ★ 3.9k • written 4.0 years ago by • 0
1
vote
3
replies
1.3k
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 5 months ago by ▴ 730 • written 3.0 years ago by • 0
0
votes
2
replies
531
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
8 months ago • updated 7 months ago yr542 • 0
0
votes
2
replies
1.2k
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 10 months ago by • 0 • written 3.1 years ago by • 0
0
votes
2
replies
2.0k
views
Creating a qPCRset object from a text file
qPCRset object nondetects r package txt
updated 6 months ago by • 0 • written 6.3 years ago by • 0
1
vote
2
replies
577
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl R biomaRt
8 months ago Miguel • 0
0
votes
1
reply
484
views
DEseq2 Single cell data paired design
R
updated 11 months ago by ▴ 30 • written 11 months ago by • 0
0
votes
1
reply
613
views
Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 11 months ago by 50k • written 11 months ago by • 0
0
votes
1
reply
1.4k
views
Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG GAGE NaN R DESeq2
updated 11 months ago by • 0 • written 5.5 years ago by • 0
0
votes
1
reply
501
views
Gene enrichment analysis
analysis R GOfuncR
updated 10 months ago by ▴ 730 • written 10 months ago by • 0
0
votes
0
replies
104
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R ATACseqQC
6 weeks ago danalvoronov ▴ 10
0
votes
0
replies
206
views
multipollutant models
statistics Regression r limma
4 months ago Jitendra ▴ 10
36 results • Page 1 of 1
Recent ...
Replies
Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq by wichaidi • 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
Awards • All
Popular Question to paria.alipour • 0
Popular Question to Eman • 0
Popular Question to James W. MacDonald 65k
Scholar to nhaus ▴ 30
Popular Question to shepherl 3.8k
Locations • All
United States, just now
WEHI, Melbourne, Australia, 7 minutes ago
France, 18 minutes ago
France, 31 minutes ago
Macao, 47 minutes ago
Traffic: 544 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