4
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7
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2.8k
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Understanding the output of the exprs() function
affymetrix microarrays
updated 9.7 years ago by 68k • written 9.7 years ago by • 0
2
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Error during installation of ChemmineOB R package
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updated 9.7 years ago by ★ 1.7k • written 9.7 years ago by ▴ 10
1
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4
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rtrackylayer import bedpe error
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updated 9.7 years ago by ★ 11k • written 9.7 years ago by ▴ 200
2
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1
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How does csaw handle multiply aligned reads?
csaw chip-seq
updated 9.7 years ago by ★ 29k • written 9.7 years ago by ▴ 40
1
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2
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how to convert emsembl identiers with ENTERz ID in a logfoldchange files generated by DESeq2 to be used for SPIA
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updated 9.7 years ago by 43k • written 9.7 years ago by • 0
4
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LIMMA gives different logFC
limma LogFC
updated 9.7 years ago by ★ 29k • written 9.7 years ago by • 0
0
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5
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Install SomaticSignatures (ERROR: compilation failed for package 'RBGL')
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9.7 years ago user31888 ▴ 30
1
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4
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Error with wavClusteR annotateClusters function
wavcluster
updated 9.7 years ago by ▴ 100 • written 9.7 years ago by ▴ 10
0
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1
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1.9k
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DEXSeq and shrinkage diagnostic : Comparison between results in plotDispEsts( dxd )
dexseq estimatedispersions
updated 9.7 years ago by ★ 13k • written 9.7 years ago by • 0
0
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1
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1.6k
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interpreting dispersion estimation in dexseq
deseq2 dexseq estimatedispersions
updated 9.7 years ago by ★ 13k • written 9.7 years ago by ★ 1.5k
2
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4
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supportedUCSCtables(genome="hg38"): Is ensGene track really available?
genomicfeatures
updated 9.7 years ago by 16k • written 9.7 years ago by ▴ 40
4
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10
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Extremely Big Number of Differences from Multi-level Design in RNA-seq Analysis by both Limma and DESeq2 - Something wrong with the design?
limma deseq2
updated 9.7 years ago by ★ 29k • written 9.7 years ago by ▴ 10
1
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7
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getting error with DEseq2
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9.7 years ago Nemo ▴ 80
0
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1
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998
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genome searching with Biostrings and the BSgenome data packages
biostrings
updated 9.7 years ago by 25k • written 9.7 years ago by • 0
0
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2
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Advice on normalization with metagenomics data
metagenome normalization metagenomics
9.7 years ago David ▴ 860
2
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30
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create design matrix when 2 groups of gene-expression data
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10.0 years ago • updated 9.7 years ago mheydarpour ▴ 10
0
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1
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1.9k
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How to identify the microarray annotation library automatically from GEO study ID?
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updated 9.7 years ago by 68k • written 9.7 years ago by • 0
0
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1
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Problem loading minfi on macOS
minfi minfidata rgl. mac os x el capitan
updated 9.7 years ago by ★ 6.5k • written 9.7 years ago by • 0
6
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6
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genefilter filtered out 60% of the original genes?
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updated 9.7 years ago by ▴ 180 • written 9.7 years ago by ▴ 20
0
votes
1
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1.3k
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Possible bug in ConsensusSequence
DECIPHER
updated 9.7 years ago by ▴ 10 • written 9.7 years ago by • 0
0
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3
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2.1k
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GSVA (1.18.0) segfaulting on small dataset
gsva segfault
updated 9.7 years ago by ★ 3.4k • written 9.7 years ago by ▴ 120
1
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3
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1.6k
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DESeq2 robust fpkm error with tximport
DESeq2
updated 9.7 years ago by 43k • written 9.7 years ago by • 0
0
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0
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1.0k
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normalizing gene expression data with TCGAbiolinks
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9.7 years ago Fernando • 0
1
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1
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1.8k
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Error using nsFilter() Error in (function (classes, fdef, mtable) unable to find an inherited method for function columns for signature function
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9.7 years ago Lucy • 0
1
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2
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1.8k
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mRNA start used instead of gene start in makeTxDbFromGFF
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updated 9.7 years ago by 16k • written 9.7 years ago by ▴ 80
2
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1
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1.4k
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Error in score() function on pairwiseAlignment()
biostrings pairwisealignment
updated 9.7 years ago by 4.3k • written 9.7 years ago by • 0
3
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5
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Wgcna with missing values - error with calculation of bicor correlations in pickSoftThreshold and blockwiseModules
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10.1 years ago • updated 9.7 years ago dvillarlozano ▴ 10
0
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5
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arrayExpress: problem running code from the vignette
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9.7 years ago kevin.rue ▴ 350
1
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5
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openCyto - flowclust.2d throws errors
opencyto flow cytometry
updated 9.7 years ago by • 0 • written 9.7 years ago by ▴ 30
0
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1
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1.4k
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Error in value[[3L]](cond) : Request to BioMart web service failed.
biomart
9.7 years ago methylUser ▴ 10
1
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3
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csaw: dumpPE on multiple bam files.
csaw dumpPE windowCounts
10.1 years ago • updated 9.7 years ago asif.zubair • 0
3
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0
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News: Bioconductor 3.3 is released
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4
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2
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distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
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updated 9.7 years ago by ★ 6.8k • written 9.7 years ago by ▴ 80
0
votes
3
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980
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Proper Design Matrix for Paired Samples where endpoint has multiple samples that pair to the same start sample
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updated 9.7 years ago by ★ 29k • written 9.7 years ago by • 0
1
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1
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1.2k
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csaw: post clustering description of regions
csaw mergeWindows
updated 9.7 years ago by ★ 29k • written 9.7 years ago by • 0
3
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2
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csaw: when not to dedup
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updated 4.4 years ago by • 0 • written 9.7 years ago by • 0
1
vote
5
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5.8k
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Heatmaps with replicates or triplicate data sets with counts to EdgeR, DESeq, or DESeq2
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updated 9.7 years ago by 43k • written 9.7 years ago by ▴ 10
0
votes
1
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3.0k
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reading an ".xml" file as FlowJo Workspace file
opencyto gating opencyto flowcore flowworkspace
updated 9.7 years ago by ★ 1.3k • written 9.7 years ago by • 0
0
votes
3
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3.2k
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Error from readCufflinks
cummerbund
updated 9.7 years ago by • 0 • written 11.2 years ago by • 0
2
votes
2
replies
2.2k
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Error in sqliteSendQuery(con, statement, bind.data) : error in statement: disk I/O error during HPO.db installation
R
updated 9.7 years ago by 25k • written 9.7 years ago by ▴ 10
3
votes
2
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1.1k
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How to do contrasts in CAMERA/ROMER/ROAST/etc in Limma?
limma
updated 9.7 years ago by ★ 29k • written 9.7 years ago by ▴ 420
0
votes
5
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2.8k
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DESeq2 plotCount question
deseq2
updated 9.7 years ago by 43k • written 9.7 years ago by ▴ 10
0
votes
0
replies
1.1k
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dexseq_prepare_annotation gives an empty gff file
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9.7 years ago sakura.nussbaum ▴ 10
2
votes
3
replies
2.0k
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comBat/SVA with no "variable of interest" and two batches
combat sva covariates
updated 9.7 years ago by ▴ 420 • written 9.7 years ago by • 0
1
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4
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1.5k
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Baseline comparison using "Comparisons both between and within subjects"
edgeR
updated 9.7 years ago by 53k • written 9.7 years ago by ▴ 10
0
votes
1
reply
743
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residuals.MArrayLM() ignores 'design' argument.
limma
updated 9.7 years ago by 53k • written 9.7 years ago by ▴ 50
1
vote
6
replies
2.7k
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Combining .idat and GEO data sets in minfi
minfi
9.7 years ago matts • 0
6
votes
2
replies
6.0k
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help with clusterProfiler enricher function
clusterprofiler
9.7 years ago naholi.alejandri ▴ 50
21
votes
24
replies
15k
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Problem with biomart's listMarts function
biomart bug
updated 9.7 years ago by ▴ 470 • written 10.2 years ago by ★ 2.1k
0
votes
1
reply
1.5k
views
Lumi error in importMethylIDAT
lumi methylation illumina
updated 9.7 years ago by 68k • written 9.7 years ago by • 0
46,717 results • Page 397 of 935
Recent ...
Replies
Comment: Clarification on counting in Rsubread (featureCounts) by Luca • 0
Thanks to both of you for your helpful suggestions. The counting was already strand-specific at both the exon and gene levels. I resolved …
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Have you told featureCounts to do strand-specific counting? As pointed out by Frances Turner, you can lose reads if they overlap the gene …
Answer: Clarification on counting in Rsubread (featureCounts) by Frances Turner ▴ 20
You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…
Comment: Incosistencies in buildSNNGraph() function by ATpoint ★ 5.0k
Just played with this a bit and I think it comes down to not having a fixed seed before running the leiden thingy. Same goes for PCA and UM…
Answer: Incosistencies in buildSNNGraph() function by Aaron Lun ★ 29k
The most obvious thing that comes to mind is the RNG seed. `cluster_leiden()` does some random number generation, somewhere deep in the **i…
Votes
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
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