2
votes
3
replies
2.2k
views
Keep getting this error "Warning: unable to access index for repository"?
CATALYST
updated 12 months ago by 16k • written 12 months ago by ▴ 20
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges grangeslist overlapsAny
updated 4 weeks ago by • 0 • written 8.0 years ago by ▴ 180
4
votes
8
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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
2
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2.2k
views
clusterProfiler - custom annotations
clusterProfiler
updated 4 months ago by ★ 4.0k • written 17 months ago by • 0
3
votes
16
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2.2k
views
DESeq2 - groups with biological replicates from the same patient
DESeq2
updated 3 months ago by 3.9k • written 2.9 years ago by ▴ 10
3
votes
12
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2.2k
views
t.test to determine the P-value in DESeq2
DESeq2
written 19 months ago by • 0
3
votes
5
replies
2.2k
views
Why the LogFC and delta-beta value are different in ChAMP
DNAMethylation ChAMP
updated 12 weeks ago by • 0 • written 3.4 years ago by • 0
0
votes
6
replies
2.2k
views
Error when Installing BioConductor Package ('affy')
Bioconductor Install affy
updated 6 months ago by ★ 4.1k • written 17 months 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
3
votes
6
replies
2.2k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 5 months ago by 65k • written 19 months ago by ▴ 10
0
votes
1
reply
2.1k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 9 months ago by 65k • written 9 months ago by • 0
4
votes
4
replies
2.1k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 5 months ago by 50k • written 2.4 years ago by ▴ 10
1
vote
10
replies
2.1k
views
Interprteting the phylogenomic profiles plot
syntenet synteny Network
written 18 months ago by • 0
4
votes
7
replies
2.1k
views
should statmod be a dependency of limma and not a suggests?
limma
updated 9 months ago by 50k • written 8.0 years ago by • 0
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
0
votes
11
replies
2.1k
views
globaltest question
Pathways probe affy Pathways probe affy
written 17.7 years ago by ▴ 30
0
votes
3
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2.1k
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maSigPro genes from clusters
masigpro clustering
updated 1 day ago by • 0 • written 7.9 years ago by • 0
0
votes
2
replies
2.1k
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ChAMP::champ.norm Error in champ.BMIQ(beta[, x], design.v, sampleID = colnames(beta)[x], : task 1 failed - "only defined on a data frame with all…
ChAMP methylation BMIQ
updated 6 months ago by • 0 • written 5.0 years ago by ▴ 20
0
votes
5
replies
2.1k
views
How can I limit the number of displayed genes in heatplot
heatplot enrichplot
updated 8 months ago by • 0 • written 17 months ago by • 0
15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
7 weeks ago • updated 18 days ago Chris ▴ 10
2
votes
6
replies
2.0k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 4 months ago by ★ 4.0k • written 14 months ago by ▴ 10
0
votes
14
replies
2.0k
views
Error while preprocessing raw data from methylation array using minfi package
minfi
updated 3 months ago by • 0 • written 8 months ago by • 0
0
votes
1
reply
2.0k
views
Error with phyloseq R package with Conda install
software error phyloseq anaconda
written 7.5 years ago by • 0
0
votes
5
replies
2.0k
views
Normalizing Affy Almac Xcel Array Data from CEL files
Annotation affy oligo ffpe Annotation affy oligo ffpe
written 10.4 years ago by ★ 13k
2
votes
2
replies
2.0k
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humann2 output appropriate for EdgeR or DESeq2 analysis
edger deseq2
updated 9 months ago by • 0 • written 6.4 years ago by • 0
1
vote
1
reply
2.0k
views
Help with error DiffBind
DiffBind
updated 9 months ago by ★ 5.2k • written 10 months ago by ▴ 10
2
votes
7
replies
2.0k
views
How to generate custom annotation for rat genome rn6 in ChIPQC
ChIPQC annotation rn6
updated 4 months ago by • 0 • written 3.7 years ago by • 0
5
votes
3
replies
2.0k
views
Cannot download GEOmetadb sqlite file
GEOmetadb
updated 3 months ago by • 0 • written 6.5 years ago by ▴ 10
10
votes
11
replies
2.0k
views
tximport error: vroom
tximport
updated 6 months ago by • 0 • written 7 months ago by ▴ 40
0
votes
4
replies
2.0k
views
Subtracting INPUT reads from ChIP read counts.
diffbind ChIP-seq
updated 3 months ago by ★ 5.2k • written 7.9 years ago by • 0
1
vote
4
replies
2.0k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 7 months ago by • 0 • written 3.2 years ago by • 0
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
1
vote
1
reply
2.0k
views
Tutorial: Update gene symbols in GeneSetCollection
gseabase msigdb genesetcollection Tutorial
written 5.9 years ago by ▴ 170
5
votes
5
replies
2.0k
views
Archive location for Bioconductor packages
archive
updated 9 months ago by 3.9k • written 21 months ago by ▴ 20
2
votes
5
replies
1.9k
views
Problem at champ.load
ChAMPdata ChAMP
updated 9 weeks ago by 65k • written 13 months ago by • 0
8
votes
13
replies
1.9k
views
Interpret plot from DiffBind
DiffBind
updated 11 months ago by ★ 5.2k • written 11 months ago by ▴ 10
5
votes
6
replies
1.9k
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Questions about using training sets and WGCNA module eigengenes generated separately for Pigengene package
Pigengene
6 months ago • updated 5 months ago kjngo ▴ 40
3
votes
6
replies
1.9k
views
Why NanoStringDiff package so slow?
NanoStringDiff NanoString nCounter DE analysis
updated 6 months ago by • 0 • written 4.8 years ago by ▴ 50
1
vote
3
replies
1.9k
views
Making MDS plot
plotMDS limma
updated 11 months ago by 50k • written 11 months ago by • 0
1
vote
3
replies
1.9k
views
DeSEQ 2 Error: some values in assay are negative
Countmatrix negativeassay DESeq2
11 months ago dania.khalid • 0
0
votes
5
replies
1.9k
views
DESeq LRT test and construction of Co-expression network
LRT co-expression network deseq2 time course experiment network analysis
updated 11 months ago by • 0 • written 6.2 years ago by ▴ 30
0
votes
4
replies
1.9k
views
how to save subsetted GDS file
gwastools
written 6.0 years ago by ▴ 30
1
vote
3
replies
1.9k
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 3 months ago by • 0 • written 23 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
4
votes
13
replies
1.9k
views
Speeding up of DelayedArray::write_block()
HDF5Array DelayedArray
updated 7 months ago by 16k • written 2.7 years ago by ▴ 10
11
votes
4
replies
1.9k
views
LIMMA dupcor() function time issue.
limma microarray block
updated 7 months ago by 50k • written 5.3 years ago by • 0
3
votes
1
reply
1.9k
views
TwoSampleMR and ieugwasr
ieugwasr clumping TwoSampleMR
updated 9 weeks ago by ▴ 10 • written 2.2 years ago by ▴ 90
10
votes
10
replies
1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 2 days ago by ▴ 220 • written 6.7 years ago by ▴ 80
3
votes
7
replies
1.9k
views
Installing densvis on a Singularity container
densvis docker
updated 11 months ago by ▴ 160 • written 12 months ago by 65k
1
vote
6
replies
1.9k
views
Rsubread - Error on buildindex - big ref sequence
Rsubread
updated 9 months ago by ▴ 380 • written 4.2 years ago by • 0
1,739 results • Page 4 of 35
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Replies
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: 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?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
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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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