1
vote
5
replies
16k
views
Limma LogFC hand calculation
limma logfc
updated 9.7 years ago by ★ 29k • written 9.7 years ago by • 0
2
votes
8
replies
2.4k
views
Regarding Somatic Mutation Signature
somaticsignatures
updated 9.7 years ago by ★ 1.3k • written 9.7 years ago by ▴ 10
4
votes
7
replies
2.8k
views
Understanding the output of the exprs() function
affymetrix microarrays
updated 9.7 years ago by 68k • written 9.7 years ago by • 0
2
votes
2
replies
3.1k
views
Error during installation of ChemmineOB R package
Chemmine Ubuntu OpenBabel
updated 9.7 years ago by ★ 1.7k • written 9.7 years ago by ▴ 10
1
vote
4
replies
1.6k
views
rtrackylayer import bedpe error
rtracklayer
updated 9.7 years ago by ★ 11k • written 9.7 years ago by ▴ 200
2
votes
1
reply
1.4k
views
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
vote
2
replies
2.2k
views
how to convert emsembl identiers with ENTERz ID in a logfoldchange files generated by DESeq2 to be used for SPIA
runspia deseq2 ENTerz
updated 9.7 years ago by 43k • written 9.7 years ago by • 0
4
votes
9
replies
3.3k
views
LIMMA gives different logFC
limma LogFC
updated 9.7 years ago by ★ 29k • written 9.7 years ago by • 0
0
votes
5
replies
2.4k
views
Install SomaticSignatures (ERROR: compilation failed for package 'RBGL')
somaticsignatures RGBL
9.7 years ago user31888 ▴ 30
1
vote
4
replies
1.8k
views
Error with wavClusteR annotateClusters function
wavcluster
updated 9.7 years ago by ▴ 100 • written 9.7 years ago by ▴ 10
0
votes
1
reply
1.9k
views
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
votes
1
reply
1.6k
views
interpreting dispersion estimation in dexseq
deseq2 dexseq estimatedispersions
updated 9.7 years ago by ★ 13k • written 9.7 years ago by ★ 1.5k
2
votes
4
replies
2.3k
views
supportedUCSCtables(genome="hg38"): Is ensGene track really available?
genomicfeatures
updated 9.7 years ago by 16k • written 9.7 years ago by ▴ 40
4
votes
10
replies
1.8k
views
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
vote
7
replies
26k
views
getting error with DEseq2
deseq2
9.7 years ago Nemo ▴ 80
0
votes
1
reply
998
views
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
votes
2
replies
2.7k
views
Advice on normalization with metagenomics data
metagenome normalization metagenomics
9.7 years ago David ▴ 860
2
votes
30
replies
5.7k
views
create design matrix when 2 groups of gene-expression data
limma
10.0 years ago • updated 9.7 years ago mheydarpour ▴ 10
0
votes
1
reply
1.9k
views
How to identify the microarray annotation library automatically from GEO study ID?
limma microarray annotation bioconductor annotate
updated 9.7 years ago by 68k • written 9.7 years ago by • 0
0
votes
1
reply
1.9k
views
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
votes
6
replies
2.5k
views
genefilter filtered out 60% of the original genes?
genefilter edgeR
updated 9.7 years ago by ▴ 180 • written 9.7 years ago by ▴ 20
0
votes
1
reply
1.3k
views
Possible bug in ConsensusSequence
DECIPHER
updated 9.7 years ago by ▴ 10 • written 9.7 years ago by • 0
0
votes
3
replies
2.1k
views
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
vote
3
replies
1.6k
views
DESeq2 robust fpkm error with tximport
DESeq2
updated 9.7 years ago by 43k • written 9.7 years ago by • 0
0
votes
0
replies
1.0k
views
normalizing gene expression data with TCGAbiolinks
microarray tcgabiolinks rnaseq
9.7 years ago Fernando • 0
1
vote
1
reply
1.8k
views
Error using nsFilter() Error in (function (classes, fdef, mtable) unable to find an inherited method for function columns for signature function
genefilter
9.7 years ago Lucy • 0
1
vote
2
replies
1.8k
views
mRNA start used instead of gene start in makeTxDbFromGFF
maketxdbfromgff genomicfeatures
updated 9.7 years ago by 16k • written 9.7 years ago by ▴ 80
2
votes
1
reply
1.4k
views
Error in score() function on pairwiseAlignment()
biostrings pairwisealignment
updated 9.7 years ago by 4.3k • written 9.7 years ago by • 0
3
votes
5
replies
9.3k
views
Wgcna with missing values - error with calculation of bicor correlations in pickSoftThreshold and blockwiseModules
software error rnaseq wgcna missing data
10.1 years ago • updated 9.7 years ago dvillarlozano ▴ 10
0
votes
5
replies
2.6k
views
arrayExpress: problem running code from the vignette
arrayexpress
9.7 years ago kevin.rue ▴ 350
1
vote
5
replies
2.4k
views
openCyto - flowclust.2d throws errors
opencyto flow cytometry
updated 9.7 years ago by • 0 • written 9.7 years ago by ▴ 30
0
votes
1
reply
1.4k
views
Error in value[[3L]](cond) : Request to BioMart web service failed.
biomart
9.7 years ago methylUser ▴ 10
1
vote
3
replies
1.5k
views
csaw: dumpPE on multiple bam files.
csaw dumpPE windowCounts
10.1 years ago • updated 9.7 years ago asif.zubair • 0
3
votes
0
replies
1.4k
views
News: Bioconductor 3.3 is released
release announcement News
9.7 years ago Dan Tenenbaum ★ 8.2k
4
votes
2
replies
1.8k
views
distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
genomicfeatures txdb maketxdbfromgff metadata
updated 9.7 years ago by ★ 6.8k • written 9.7 years ago by ▴ 80
0
votes
3
replies
980
views
Proper Design Matrix for Paired Samples where endpoint has multiple samples that pair to the same start sample
edger design matrix
updated 9.7 years ago by ★ 29k • written 9.7 years ago by • 0
1
vote
1
reply
1.2k
views
csaw: post clustering description of regions
csaw mergeWindows
updated 9.7 years ago by ★ 29k • written 9.7 years ago by • 0
3
votes
2
replies
1.6k
views
csaw: when not to dedup
csaw dedup
updated 4.4 years ago by • 0 • written 9.7 years ago by • 0
1
vote
5
replies
5.8k
views
Heatmaps with replicates or triplicate data sets with counts to EdgeR, DESeq, or DESeq2
heatmap.2 heatmap edgeR deseq2 deseq
updated 9.7 years ago by 43k • written 9.7 years ago by ▴ 10
0
votes
1
reply
3.0k
views
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
replies
3.2k
views
Error from readCufflinks
cummerbund
updated 9.7 years ago by • 0 • written 11.2 years ago by • 0
2
votes
2
replies
2.2k
views
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
replies
1.1k
views
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
replies
2.8k
views
DESeq2 plotCount question
deseq2
updated 9.7 years ago by 43k • written 9.7 years ago by ▴ 10
0
votes
0
replies
1.1k
views
dexseq_prepare_annotation gives an empty gff file
dexseq prepare annotation empty gff
9.7 years ago sakura.nussbaum ▴ 10
2
votes
3
replies
2.0k
views
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
vote
4
replies
1.5k
views
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
views
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
views
Combining .idat and GEO data sets in minfi
minfi
9.7 years ago matts • 0
6
votes
2
replies
6.0k
views
help with clusterProfiler enricher function
clusterprofiler
9.7 years ago naholi.alejandri ▴ 50
46,719 results • Page 397 of 935
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Comment: Development of MSstat workflow to analyze DIA time series data by Gordon Smyth 53k
Are there any other explanatory factors or covariates in your experiment other than time point? Do you have biological replicates at each t…
Answer: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Either of these choices is perfectly acceptable from an edgeR analysis point of view, it is more to do with which is more relevant for your…
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Your follow-up question is very much wider than the first, and is essentially a research question rather a software question. As one of the…
Comment: Error in creating BSGenome package by Nguyen • 0
I keep running into this error, please help: ``` Writing all sequences to './BSgenome.Panubis.NCBI.Panubis1.0/inst/extdata/single_sequenc…
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…
Votes
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
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)
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