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3
votes
4
replies
3.6k
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RNAseq analysis using edgeR - specifying and testing full factorial 2x2x4 model, main effects and interactions.
edger
multiple factor design
interactions
updated 10.7 years ago by
Aaron Lun
★ 29k • written 10.7 years ago by
v.oostra
• 0
1
vote
5
replies
3.0k
views
GEOquery getGeo line 1 didn't have 6 elements
GEOquery error message
updated 10.7 years ago by
Sean Davis
21k • written 10.7 years ago by
jianwang2010
▴ 10
4
votes
2
replies
3.1k
views
diffBind correlation plot
diffbind
10.7 years ago
yijing.su
• 0
0
votes
2
replies
1.8k
views
EBSeq package gives NaN Values for EBMultiTest
differential expression
ebseq
rnaseq
10.7 years ago
jbarker2
• 0
0
votes
1
reply
1.4k
views
riboSeqR: legend in plotFS
riboseqr
updated 10.7 years ago by
Thomas J Hardcastle
▴ 180 • written 10.7 years ago by
antonvila.s
• 0
2
votes
6
replies
4.3k
views
DiffBind: reading in peaksets generated by Homer2
diffbind
updated 10.7 years ago by
sergio.espeso-gil
• 0 • written 11.0 years ago by
iliya.lefterov
▴ 10
0
votes
0
replies
1.9k
views
Differential expression workflow for alternative splicing
dexseq
bitseq
spliceR
10.7 years ago
elle
▴ 10
0
votes
1
reply
2.0k
views
RNASeq time-course analysis with maSigPro: T.fit error when assessing multiple groups
rnaseq
masigpro
timecourse
10.7 years ago
Ryan Goosen
• 0
1
vote
5
replies
5.3k
views
Converting a DNAStringSetList to characters quickly
readVcf
DNAStringSet
DNAStringSetList
variantannotation
readvcf
10.7 years ago
dan.gatti
• 0
4
votes
21
replies
5.0k
views
RMA normaliztion using XPS
normalization
xps
updated 10.7 years ago by
cstrato
★ 3.9k • written 10.8 years ago by
dhwani.dholakia
• 0
2
votes
2
replies
5.0k
views
Help with installing biocLite.R
biocLite
biocinstaller
10.7 years ago
thomas.mohr
▴ 20
0
votes
4
replies
2.5k
views
rhdf5 segfault on write of large matrix
rhdf5
segfault
10.7 years ago
Kort, Eric
▴ 220
0
votes
0
replies
2.7k
views
TCGA RSEM normalized RNAseqV2 counts
normalization
cancer
tcga
10.7 years ago
ezz
• 0
1
vote
10
replies
3.9k
views
Attributes construct error in biomaRt
biomart
updated 10.7 years ago by
Steffen Durinck
▴ 90 • written 10.7 years ago by
sean.taylor
• 0
0
votes
4
replies
2.2k
views
Use of confounders in downstream analysis
limma
GSA
confounding
within-pair analysis
450k
10.7 years ago
Aileen Bahl
▴ 10
1
vote
3
replies
2.4k
views
lumiR.batch fails after upgrade to R v3.2.0 and lumi v2.20.0
lumi
10.7 years ago
Jeremy Martinson
• 0
3
votes
11
replies
15k
views
Problems updating Bioconductor with R 3.2.0
upgrade
r update
updated 10.7 years ago by
Dan Tenenbaum
★ 8.2k • written 10.7 years ago by
daniil.sarkisyan
▴ 10
3
votes
5
replies
1.8k
views
affycoretools' plotPCA no longer can do 3D plot?
affycoretools
updated 10.7 years ago by
James W. MacDonald
68k • written 10.7 years ago by
Jenny Drnevich
★ 2.0k
0
votes
1
reply
984
views
MA plot error
rnaseq
updated 10.7 years ago by
James W. MacDonald
68k • written 10.7 years ago by
pablo_calza
• 0
0
votes
1
reply
3.6k
views
Warning in lfproc when using rlog or varianceStabilisingTransformation from DESeq2
DESeq2
rlog
varianceStabilizingTransformation
lfproc
updated 10.7 years ago by
Michael Love
43k • written 10.7 years ago by
katja
• 0
1
vote
4
replies
2.8k
views
How to get from xcmsRaw to a xcmsSet
xcms
metabolomics
updated 10.7 years ago by
Thomas Lin Pedersen
▴ 70 • written 10.7 years ago by
Johannes Rainer
★ 2.1k
0
votes
0
replies
2.0k
views
what R package prediction secondary structure for amino acids
packages
10.7 years ago
m016648
• 0
0
votes
0
replies
933
views
Trouble to load data with basicProfile
go
software error
annotation
10.7 years ago
ncervea
• 0
4
votes
5
replies
6.4k
views
decideTests() options in LIMMA
limma
B stats
decideTests
updated 3.4 years ago by
chm
• 0 • written 10.7 years ago by
Elsa
• 0
0
votes
1
reply
1.6k
views
Mixing list from Piano package output
Piano
List
updated 10.7 years ago by
Leif Väremo
▴ 70 • written 10.7 years ago by
nonCodingGene
▴ 10
1
vote
5
replies
2.7k
views
Appropriate merge of batches of the same array to create a final total ExpressionSet
frma
bioconductor
batcheffect
Primeview
insilicomerging
updated 10.7 years ago by
Matthew McCall
▴ 830 • written 10.7 years ago by
svlachavas
▴ 840
4
votes
2
replies
6.1k
views
Mapping KEGG pathway names to IDs using KEGG.db package
KEGG.db
KEGG id
updated 10.7 years ago by
Martin Morgan
25k • written 10.7 years ago by
NS
▴ 60
3
votes
12
replies
3.3k
views
Error installing cn.mops and Rsamtools in R 3.1.3
rsamtools
cn.mops
installation
10.8 years ago • updated 10.7 years ago
Spollen, William G.
▴ 30
0
votes
0
replies
1.4k
views
Using maPredictDSC with Illumina bead chip
maPredictDSC
illumina beadchip
10.7 years ago
sanj
▴ 20
0
votes
0
replies
1.2k
views
legend in plotFS
riboseqr
10.7 years ago
antonvila.s
• 0
2
votes
5
replies
3.7k
views
miRNA expression analysis : annotation
miRNA
annotation
affymetrixchip
10.8 years ago • updated 10.7 years ago
aswathym
▴ 10
0
votes
1
reply
5.0k
views
ERROR: lazy loading failed for package ‘org.Hs.eg.db’
org.hs.eg.db
annotationdbi
error
updated 10.7 years ago by
Dan Tenenbaum
★ 8.2k • written 10.7 years ago by
tina.khajeh
• 0
0
votes
1
reply
2.7k
views
Analyzing 450k Methylation from TCGA Website
minfidata
minfi
illuminahumanmethylation450k.db
illuminahumanmethylation450kanno.ilmn12.hg19
10.7 years ago
alejandretheodore
• 0
0
votes
7
replies
2.8k
views
metagenomeSeq cumNorm issue with NAs in real data
metagenomeseq
updated 10.7 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 10.8 years ago by
carr0603
• 0
3
votes
6
replies
2.2k
views
error using org.Hs.eg.db package : Error in get(load(file)) :
org.hs.eg.db
select
10.7 years ago
tina.khajeh
• 0
1
vote
8
replies
2.6k
views
boxplot, microarray, hugene 2.0 st
boxplot
microarray
pd.hugene.2.0.st
10.8 years ago • updated 10.7 years ago
kanacska
▴ 10
3
votes
3
replies
1.9k
views
Correlation/clustering of numeric (continuous) and categorical values
correlation
updated 10.7 years ago by
Sean Davis
21k • written 10.8 years ago by
Johannes Rainer
★ 2.1k
1
vote
2
replies
12k
views
select() gene in db not working although key exists
annotationdbi
org.mm.eg.db
org.dm.eg.db
select
10.7 years ago
Patrick Schorderet
▴ 20
7
votes
9
replies
2.4k
views
codelink package is not installing
codelink
r
10.7 years ago
Agaz Hussain Wani
▴ 260
0
votes
1
reply
1.0k
views
Best way to load .cel files so as it consumes less memory
affy
read in cel files
updated 10.7 years ago by
svlachavas
▴ 840 • written 10.7 years ago by
dhwani.dholakia
• 0
5
votes
6
replies
7.9k
views
Importing a .txt file with multiple headers into R
input files
read.table
maxmatch
Mummer
updated 10.7 years ago by
Malcolm Cook
★ 1.6k • written 10.7 years ago by
a.afshinfard
▴ 10
0
votes
0
replies
1.0k
views
pssm for r language
microarray
10.7 years ago
m016648
• 0
7
votes
4
replies
8.1k
views
Low percentage of assigned fragments with FeatureCounts
rsubread
featurecounts
rnaseq
10.7 years ago
beiting
▴ 30
0
votes
0
replies
1.3k
views
News:
Bioconductor 3.1 is released!
release
News
10.7 years ago
Dan Tenenbaum
★ 8.2k
0
votes
1
reply
2.1k
views
Reading in and normalising ht-hgu133a and hgu133a files together
hgu133a
rma
normalization
affy
updated 10.7 years ago by
svlachavas
▴ 840 • written 10.8 years ago by
parisa_1986
• 0
2
votes
11
replies
6.7k
views
MA Plot colors
MA Plot
updated 10.7 years ago by
James W. MacDonald
68k • written 10.7 years ago by
pablo_calza
• 0
1
vote
0
replies
1.2k
views
ImportC function Problem
importing
10.7 years ago
gugpuccio
▴ 10
1
vote
4
replies
2.1k
views
IRanges missing S4Vectors_defines.h
iranges
s4vectors
updated 10.7 years ago by
Hervé Pagès
16k • written 10.8 years ago by
Nathan Sheffield
▴ 20
3
votes
7
replies
5.3k
views
miRNA microarray analysis
microarray
cdf
updated 10.8 years ago by
Gordon Smyth
53k • written 10.8 years ago by
aswathym
▴ 10
0
votes
6
replies
2.6k
views
rtracklayer issue: Tracks don't show up
rtracklayer
bug
session
updated 10.8 years ago by
Michael Lawrence
★ 11k • written 10.8 years ago by
chrarnold
• 0
46,717 results • Page
461 of 935
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Comment: Joining different datasets and analyzing using the group-specific condition effe
by
jason.chai
• 0
@mikelove Could I please ask if a similar method would work my set of samples? I have 255 samples which have been generated from 76 subject…
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…
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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