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1
vote
5
replies
16k
views
Limma LogFC hand calculation
limma
logfc
updated 9.7 years ago by
Aaron Lun
★ 29k • written 9.7 years ago by
cookm346
• 0
2
votes
8
replies
2.4k
views
Regarding Somatic Mutation Signature
somaticsignatures
updated 9.7 years ago by
Julian Gehring
★ 1.3k • written 9.7 years ago by
sj1
▴ 10
4
votes
7
replies
2.8k
views
Understanding the output of the exprs() function
affymetrix microarrays
updated 9.7 years ago by
James W. MacDonald
68k • written 9.7 years ago by
neverstop
• 0
2
votes
2
replies
3.1k
views
Error during installation of ChemmineOB R package
Chemmine
Ubuntu
OpenBabel
updated 9.7 years ago by
Thomas Girke
★ 1.7k • written 9.7 years ago by
elisa.micarelli
▴ 10
1
vote
4
replies
1.6k
views
rtrackylayer import bedpe error
rtracklayer
updated 9.7 years ago by
Michael Lawrence
★ 11k • written 9.7 years ago by
tangming2005
▴ 200
2
votes
1
reply
1.4k
views
How does csaw handle multiply aligned reads?
csaw
chip-seq
updated 9.7 years ago by
Aaron Lun
★ 29k • written 9.7 years ago by
endrebak85
▴ 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
Michael Love
43k • written 9.7 years ago by
saamar.rajput
• 0
4
votes
9
replies
3.3k
views
LIMMA gives different logFC
limma
LogFC
updated 9.7 years ago by
Aaron Lun
★ 29k • written 9.7 years ago by
beginner
• 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
federico.comoglio
▴ 100 • written 9.7 years ago by
S.k
▴ 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
Wolfgang Huber
★ 13k • written 9.7 years ago by
julie.sedbon
• 0
0
votes
1
reply
1.6k
views
interpreting dispersion estimation in dexseq
deseq2
dexseq
estimatedispersions
updated 9.7 years ago by
Wolfgang Huber
★ 13k • written 9.7 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
4
replies
2.3k
views
supportedUCSCtables(genome="hg38"): Is ensGene track really available?
genomicfeatures
updated 9.7 years ago by
Hervé Pagès
16k • written 9.7 years ago by
Chao-Jen Wong
▴ 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
Aaron Lun
★ 29k • written 9.7 years ago by
dustar1986
▴ 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
Martin Morgan
25k • written 9.7 years ago by
mike_and_dan
• 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
James W. MacDonald
68k • written 9.7 years ago by
lijin.abc
• 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
Kasper Daniel Hansen
★ 6.5k • written 9.7 years ago by
holbrookjoanna
• 0
6
votes
6
replies
2.5k
views
genefilter filtered out 60% of the original genes?
genefilter
edgeR
updated 9.7 years ago by
Nikos Ignatiadis
▴ 180 • written 9.7 years ago by
cafelumiere12
▴ 20
0
votes
1
reply
1.3k
views
Possible bug in ConsensusSequence
DECIPHER
updated 9.7 years ago by
Erik Wright
▴ 10 • written 9.7 years ago by
rob.lanfear
• 0
0
votes
3
replies
2.1k
views
GSVA (1.18.0) segfaulting on small dataset
gsva
segfault
updated 9.7 years ago by
Robert Castelo
★ 3.4k • written 9.7 years ago by
Rajarshi Guha
▴ 120
1
vote
3
replies
1.6k
views
DESeq2 robust fpkm error with tximport
DESeq2
updated 9.7 years ago by
Michael Love
43k • written 9.7 years ago by
GWW
• 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
Hervé Pagès
16k • written 9.7 years ago by
TimothéeFlutre
▴ 80
2
votes
1
reply
1.4k
views
Error in score() function on pairwiseAlignment()
biostrings
pairwisealignment
updated 9.7 years ago by
shepherl
4.3k • written 9.7 years ago by
jdydu
• 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
bmuchmore
• 0 • written 9.7 years ago by
Ulrik Stervbo
▴ 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
Valerie Obenchain
★ 6.8k • written 9.7 years ago by
TimothéeFlutre
▴ 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
Aaron Lun
★ 29k • written 9.7 years ago by
laura
• 0
1
vote
1
reply
1.2k
views
csaw: post clustering description of regions
csaw
mergeWindows
updated 9.7 years ago by
Aaron Lun
★ 29k • written 9.7 years ago by
asif.zubair
• 0
3
votes
2
replies
1.6k
views
csaw: when not to dedup
csaw
dedup
updated 4.4 years ago by
uli.arb
• 0 • written 9.7 years ago by
asif.zubair
• 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
Michael Love
43k • written 9.7 years ago by
Zain A Alvi
▴ 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
Jiang, Mike
★ 1.3k • written 9.7 years ago by
anara92
• 0
0
votes
3
replies
3.2k
views
Error from readCufflinks
cummerbund
updated 9.7 years ago by
dusan.randjelovic
• 0 • written 11.2 years ago by
HamidahR
• 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
Martin Morgan
25k • written 9.7 years ago by
brlee0920
▴ 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
Aaron Lun
★ 29k • written 9.7 years ago by
chris86
▴ 420
0
votes
5
replies
2.8k
views
DESeq2 plotCount question
deseq2
updated 9.7 years ago by
Michael Love
43k • written 9.7 years ago by
Antonio Ahn
▴ 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
chris86
▴ 420 • written 9.7 years ago by
TP
• 0
1
vote
4
replies
1.5k
views
Baseline comparison using "Comparisons both between and within subjects"
edgeR
updated 9.7 years ago by
Gordon Smyth
53k • written 9.7 years ago by
dustar1986
▴ 10
0
votes
1
reply
743
views
residuals.MArrayLM() ignores 'design' argument.
limma
updated 9.7 years ago by
Gordon Smyth
53k • written 9.7 years ago by
Gregory Warnes
▴ 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
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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
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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…
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by
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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
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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…
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A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
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