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3
votes
3
replies
13k
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How to fix 'long vectors not supported yet' error in R
r
updated 6 weeks ago by • 0 • written 5.3 years ago by • 0
10
votes
10
replies
7.4k
views
biomaRt not working - lazy table error
error lazy R biomaRt table
updated 8 weeks ago by • 0 • written 6 months ago by ▴ 10
0
votes
5
replies
9.3k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 8 weeks ago by • 0 • written 7.6 years ago by • 0
0
votes
10
replies
846
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R BioMart biomaRt
6 months ago • updated 11 weeks ago ScafioRuo • 0
0
votes
0
replies
126
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R ATACseqQC
11 weeks ago danalvoronov ▴ 10
0
votes
4
replies
393
views
limma with interaction term
R biostatistics limma Epigenetics
3 months ago • updated 11 weeks ago Jitendra ▴ 10
2
votes
4
replies
3.8k
views
How to convert large gene counts data into matrix?
R Bioconductor singlecell bioinformatics seurat
updated 3 months ago by 50k • written 4.8 years ago by • 0
1
vote
12
replies
2.5k
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 3 months ago by • 0 • written 2.6 years ago by ▴ 380
0
votes
6
replies
8.7k
views
No gene can be mapped error with clusterprofiler
clusterprofiler r
updated 4 months ago by ★ 4.0k • written 7.3 years ago by • 0
0
votes
3
replies
520
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
updated 5 months ago by • 0 • written 5 months ago by • 0
1
vote
3
replies
1.9k
views
DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind R chipseq
updated 5 months ago by ★ 5.2k • written 6.6 years ago by • 0
0
votes
3
replies
1.7k
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R oligoClasses Oligoclass Bioconductor Oligo
written 3.2 years ago by • 0
1
vote
5
replies
2.2k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 9.3 years ago by ▴ 10
0
votes
0
replies
246
views
multipollutant models
statistics Regression r limma
5 months ago Jitendra ▴ 10
3
votes
4
replies
559
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
5 months ago pl23 • 0
1
vote
3
replies
1.4k
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 6 months ago by ▴ 730 • written 3.0 years ago by • 0
22
votes
15
replies
7.6k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 6 months ago by ▴ 10 • written 2.1 years ago by ▴ 50
0
votes
2
replies
2.1k
views
Creating a qPCRset object from a text file
qPCRset object nondetects r package txt
updated 7 months ago by • 0 • written 6.3 years ago by • 0
7
votes
5
replies
7.1k
views
biomaRt server error, and mirrors do not help
ensembl biomaRt R
updated 7 months ago by • 0 • written 2.0 years ago by ▴ 40
4
votes
5
replies
2.0k
views
time course microarray data ArrayExpress database
R GillespieColin ArrayExpress import TimeSeriesExperiment
updated 7 months ago by ▴ 40 • written 19 months ago by ▴ 20
4
votes
7
replies
14k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 8 months ago by 50k • written 22 months ago by ▴ 30
0
votes
2
replies
582
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
9 months ago • updated 8 months ago yr542 • 0
1
vote
2
replies
639
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl R biomaRt
9 months ago Miguel • 0
2
votes
5
replies
1.4k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
10 months ago • updated 9 months ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
532
views
Gene enrichment analysis
analysis R GOfuncR
updated 11 months ago by ▴ 730 • written 11 months ago by • 0
3
votes
3
replies
4.8k
views
Genelist input for ClusterProfiler
R ClusterProfiler Enrichment Pathway
updated 11 months ago by ★ 4.0k • written 4.1 years ago by • 0
0
votes
2
replies
1.2k
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 11 months ago by • 0 • written 3.2 years ago by • 0
4
votes
8
replies
2.2k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 11 months ago by 50k • written 17 months ago by ▴ 20
0
votes
1
reply
1.4k
views
Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG GAGE NaN R DESeq2
updated 12 months ago by • 0 • written 5.6 years ago by • 0
0
votes
1
reply
651
views
Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 12 months ago by 50k • written 12 months ago by • 0
8
votes
11
replies
11k
views
R: error while reading .h5 files from R using rdhf5 package
rhdf5 r hdf5
updated 12 months ago by • 0 • written 6.9 years ago by ▴ 10
0
votes
1
reply
519
views
DEseq2 Single cell data paired design
R
updated 12 months ago by ▴ 30 • written 12 months ago by • 0
0
votes
4
replies
922
views
Combine RNA-seq
BatchEffect R rnaseq
updated 12 months ago by ★ 1.4k • written 13 months ago by • 0
1
vote
3
replies
889
views
tximport error
tximport r
updated 13 months ago by 42k • written 13 months ago by • 0
2
votes
4
replies
1.7k
views
make TxDb from list of genes
R maketxdbfrombiomart maketxdbfromgranges rstudio ensembl
updated 13 months ago by ▴ 10 • written 5.4 years ago by • 0
1
vote
4
replies
1.4k
views
RNA-seq analysis using R
limma rnaseq convert R
updated 13 months ago by 50k • written 5.5 years ago by ▴ 10
0
votes
4
replies
926
views
Unable to install BiocManager
Biocmanager R
updated 13 months ago by ▴ 50 • written 13 months ago by • 0
1
vote
2
replies
914
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
13 months ago Abdul ▴ 20
0
votes
0
replies
498
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
13 months ago aymanreffai • 0
1
vote
1
reply
1.3k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST pathview R
updated 13 months ago by ★ 4.0k • written 13 months ago by • 0
3
votes
2
replies
2.1k
views
How to do simple Fisher' exact test for overlapped genomic interval in R?
test fisher exact r findoverlapsofpeaks
updated 13 months ago by • 0 • written 8.4 years ago by ▴ 80
0
votes
3
replies
1.5k
views
How to extract / pull out each row(a.k.a, single genome interval ) from given bed files by row by row for meta analysis?
r bioinformatics peakset
updated 13 months ago by • 0 • written 8.4 years ago by ▴ 80
1
vote
1
reply
1.3k
views
Error in h5checktype(). H5Identifier not valid.
rhdf5 rhdf r
updated 13 months ago by • 0 • written 14 months ago by • 0
0
votes
13
replies
5.0k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
14 months ago Laia ▴ 10
0
votes
3
replies
4.0k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot R clusterProfiler
updated 14 months ago by ★ 4.0k • written 15 months ago by • 0
0
votes
1
reply
752
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 14 months ago by ▴ 740 • written 14 months ago by ▴ 10
0
votes
0
replies
482
views
rDGIdb package: score of the results
rDGIdb r
14 months ago HELEN • 0
2
votes
1
reply
530
views
add column with name in R
name R column
updated 14 months ago by ▴ 70 • written 14 months ago by • 0
0
votes
4
replies
891
views
how to extract list in quantile in R
R quantile list
14 months ago sat • 0
0
votes
0
replies
583
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival TCGAbiolinks R PAAD
14 months ago Manav • 0
50 results • Page 1 of 1
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Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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