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Votes
5
votes
6
replies
3.3k
views
extracting Allele Read Counts
rsamtools
vcf
8.7 years ago
Bogdan
▴ 670
0
votes
2
replies
6.1k
views
DESeq2: how to interpret the heatmap clustering samples
deseq2
rlog transformation
heatmap
scale
8.7 years ago
lina.faller
▴ 10
0
votes
3
replies
1.5k
views
Error in c(DataFrameList(META = meta), tbls[unique(tags)])
VariantAnnotation
updated 8.7 years ago by
Hervé Pagès
16k • written 8.7 years ago by
ddzhangzz
• 0
2
votes
12
replies
3.8k
views
biomaRt does not return entrezgene id
bioconductor
biomart
entrez gene identifiers
ensembl
ensembl mart
updated 8.7 years ago by
Thomas Maurel
▴ 800 • written 8.7 years ago by
daniel.carbajo
• 0
1
vote
5
replies
3.6k
views
Force DESeq2 to use pseudocounts
deseq2
rna-seq
8.7 years ago
manuelw
• 0
6
votes
7
replies
4.2k
views
Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with oligo for DE analysis
oligo
affycoretools
hta2.0
affymetrix
updated 3.6 years ago by
Yang Shi
▴ 10 • written 8.7 years ago by
svlachavas
▴ 840
3
votes
4
replies
1.7k
views
Does Rsamtools support tag names with number characters? i.e ."B1"
rsamtools
bug
updated 8.7 years ago by
Martin Morgan
25k • written 8.7 years ago by
joelrrv
• 0
0
votes
3
replies
3.2k
views
ChIPpeakAnno :findOverlapsOfPeaks: number for overlap peak in venn diagram is different than output of ol1$overlappingPeaks
chippeakanno
updated 8.7 years ago by
Ou, Jianhong
★ 1.3k • written 8.7 years ago by
sudhirjadhao2009
• 0
0
votes
0
replies
1.2k
views
qaProcess.timeline in flowQ won't accept filepath with spaces
flowQ
qaProcess.timeline
flowcore
8.7 years ago
hefin_8
• 0
2
votes
8
replies
6.6k
views
limma interaction contrasts
limma contrast matrix
limma design matrix
limma
updated 8.7 years ago by
Aaron Lun
★ 29k • written 8.7 years ago by
joelrome88
▴ 20
0
votes
0
replies
1.0k
views
an error in TitanCNA
TitanCNA
HMMcopy
8.7 years ago
Bogdan
▴ 670
0
votes
1
reply
2.4k
views
Different padj value after multiple testing
deseq2
padj
multiple comparisons
differential gene expression
updated 8.7 years ago by
Michael Love
43k • written 8.7 years ago by
tarun2
• 0
5
votes
3
replies
2.1k
views
Classes and methods for working with segmented copy number data
cgh
copynumber
updated 8.7 years ago by
Marcel Ramos
700 • written 9.4 years ago by
Sean Davis
21k
6
votes
4
replies
2.7k
views
Problem running dexseq in parallel using BiocParallel
dexseq
updated 8.7 years ago by
s.w.vanderlaan
▴ 30 • written 8.7 years ago by
forestylake
▴ 30
0
votes
0
replies
1.2k
views
imputing data using pcaMethods with large amounts of missing data in rows
pcamethods
missing data
8.7 years ago
eli-sava
• 0
0
votes
2
replies
1.1k
views
bestglm with DESeq2 dispersions
deseq2
8.7 years ago
kodream
▴ 20
0
votes
0
replies
2.0k
views
use control_condition in heatmap with cummeRbund
cummerbund
heatmap
8.7 years ago
domenico.somma
• 0
2
votes
1
reply
1.5k
views
Corrupt AnnotationHub database - previously posted fix not working
annotation
error
8.7 years ago
tullyij1
• 0
2
votes
3
replies
5.3k
views
Select specific variants from vcf file
vcf
updated 8.7 years ago by
Martin Morgan
25k • written 8.7 years ago by
Adam
• 0
0
votes
1
reply
1.5k
views
BiSeq - modelling options betaRegression
biseq
RRBS
betaregression
8.7 years ago
l.eijssen
• 0
1
vote
4
replies
2.5k
views
New to mass spec data analysis
data analysis
xcms
Tutorial
updated 14 months ago by
abhisek001
• 0 • written 8.7 years ago by
Dan_reichert
• 0
9
votes
4
replies
7.4k
views
Limma: Paired samples, multiple groups: problems understanding contrasts and model.matrix
microarray
limma
design and contrast matrix
8.7 years ago
Anna
▴ 50
1
vote
0
replies
1.5k
views
generate table of counts with strand-specific paired-end RNA-seq data
summarizeoverlaps
paired-end reads
readGAlignmentPairs
8.7 years ago
teresati
▴ 10
0
votes
0
replies
1.6k
views
how to use Methylumi background correction (noob) in CHAMP
Methylumi
NOOB
CHAMP
Background corection
illimina 450k methylation
8.7 years ago
rahel14350
▴ 10
0
votes
1
reply
1.5k
views
Monocle group sizes
monocle
8.7 years ago
ribioinfo
▴ 100
0
votes
0
replies
931
views
FEM Errors out after Monte Carlo Runs
FEM
8.7 years ago
mnaymik
▴ 10
0
votes
0
replies
1.6k
views
Job:
Research Scientist for Bioinformatics, University of Minnesota
R
bioconductor
next-generation sequencing
Job
8.7 years ago
mmacchie
• 0
2
votes
5
replies
2.1k
views
Error involving ChIPQCreport
ChIPQC
updated 8.7 years ago by
Thomas Carroll
▴ 420 • written 8.8 years ago by
Roger
• 0
1
vote
1
reply
908
views
Sorting the VIEW index in ascending/descending order
R
diffbind
updated 8.7 years ago by
Marcel Ramos
700 • written 8.7 years ago by
rbronste
▴ 60
0
votes
1
reply
1.6k
views
salmon quantification - identical transcripts in fasta file
salmon
updated 8.7 years ago by
James W. MacDonald
68k • written 8.7 years ago by
dmr210
▴ 30
6
votes
12
replies
7.0k
views
Error in getBM of biomaRt package
biomaRt
getBM
updated 8.7 years ago by
boris.steipe
• 0 • written 8.9 years ago by
rubi
▴ 110
0
votes
1
reply
1.2k
views
probe set-gene relation
probe
geneid
probeset
updated 8.7 years ago by
James W. MacDonald
68k • written 8.7 years ago by
basak
• 0
0
votes
1
reply
2.4k
views
R package for analysis Agilent microarray?
agilent microarrays
updated 8.7 years ago by
James W. MacDonald
68k • written 8.7 years ago by
lqfuture
• 0
0
votes
0
replies
1.5k
views
gage pca loadings
pca
gage
loadings
8.7 years ago
MT
▴ 10
0
votes
1
reply
1.5k
views
error in getsymbol function
symbol
updated 8.7 years ago by
Guido Hooiveld
★ 4.1k • written 8.7 years ago by
farahqureshi5
• 0
2
votes
6
replies
5.3k
views
Difference between fitFeatureModel and fitZIG in metagenomeSeq
metagenomeseq
8.8 years ago • updated 8.7 years ago
sasha
• 0
0
votes
1
reply
990
views
uisng image command
image
8.7 years ago
farahqureshi5
• 0
0
votes
6
replies
2.4k
views
DEXSeq Error in FUN(X[[i]], ...) : subscript out of bounds not sure why
dexseq
8.7 years ago
badribio
• 0
0
votes
0
replies
880
views
cluserRepro for IGP calculation - long running time
clusterRepro
8.7 years ago
andres.firrincieli
▴ 50
3
votes
1
reply
11k
views
Error using function NbClust regarding multiple values in the argument "index" of package NbClust for getting the optimal number of clusters of a dat…
NbClust
clustering
looping
list object
function creation
updated 8.7 years ago by
james.tsakalos
▴ 20 • written 10.3 years ago by
svlachavas
▴ 840
0
votes
1
reply
3.2k
views
How does Limma calculate the log2 fold change?
limma
updated 8.7 years ago by
Gordon Smyth
53k • written 19.6 years ago by
Groot, Philip de
▴ 630
1
vote
8
replies
7.9k
views
Limma, SAM and Fold Change Calculation
affy
limma
gcrma
siggenes
updated 8.7 years ago by
Gordon Smyth
53k • written 18.5 years ago by
Peter White
▴ 80
0
votes
2
replies
3.1k
views
Biostrings: retrieve 3'UTR sequence with Transcript
R
Biostrings
sequence
updated 8.7 years ago by
Mike Smith
★ 6.6k • written 8.7 years ago by
aspenaure
• 0
1
vote
4
replies
2.1k
views
Query Error: biomaRt
biomart
bioconductor
8.7 years ago
Jaspreet Kaur
• 0
0
votes
7
replies
3.1k
views
DESeq2 analysis with pairwise analysis and batch effect correction
deseq2
updated 8.7 years ago by
Michael Love
43k • written 8.7 years ago by
jogiles
• 0
4
votes
3
replies
5.0k
views
EdgeR on miRNA data
edger
miRNA
updated 8.7 years ago by
Aaron Lun
★ 29k • written 8.7 years ago by
melmogy
• 0
3
votes
3
replies
1.3k
views
[edgeR Usage] Constructing DGE test with fewer input variables
edger
updated 8.7 years ago by
Aaron Lun
★ 29k • written 8.7 years ago by
mousheng xu
▴ 10
0
votes
2
replies
1.3k
views
Deseq2 to nanlyse one level / condition
deseq2
updated 8.7 years ago by
James W. MacDonald
68k • written 8.7 years ago by
cardin.julie
• 0
5
votes
5
replies
2.8k
views
News:
Ensembl 88 is out!
ensembl
ensembl mart
biomart
e!88
News
8.7 years ago
Thomas Maurel
▴ 800
0
votes
0
replies
1.2k
views
crlmm for new chip?
crlmm
8.7 years ago
Scottt Hazelhurst
• 0
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C: DESeq2 Following RSEM
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Answer: Large logFC but somewhat high FDR
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