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0
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10
replies
2.5k
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Rsubread on Cygwin - error due to gcc ... -D MACOS - why?
Rsubread
updated 7.7 years ago by
Wei Shi
★ 3.6k • written 7.9 years ago by
MWSchmid
• 0
1
vote
8
replies
1.8k
views
boxplot, microarray, hugene 2.0 st
boxplot
microarray
pd.hugene.2.0.st
9.1 years ago
kanacska
▴ 10
0
votes
8
replies
1.7k
views
Problem creating a contrast matrix
updated 16.9 years ago by
James W. MacDonald
65k • written 16.9 years ago by
Siarhei Manakou
▴ 100
0
votes
10
replies
1.7k
views
Harsh results using limma!
limma
limma
updated 19.8 years ago by
A.J. Rossini
▴ 810 • written 19.8 years ago by
michael watson IAH-C
★ 3.4k
0
votes
11
replies
3.7k
views
Filtering genes using a list
updated 19.8 years ago by
James W. MacDonald
65k • written 19.8 years ago by
mcolosim@brandeis.edu
▴ 70
5
votes
18
replies
3.2k
views
Incongruencies between DEXSeq and BitSeq/Cuffdiff
dexseq
bitseq
cuffdiff
Differential exon usage
isoforms
9.0 years ago • updated 8.9 years ago
elle
▴ 10
28
votes
25
replies
5.9k
views
[FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
Gviz
rtracklayer
updated 6.8 years ago by
aina.jene
▴ 10 • written 7.3 years ago by
Ramiro Magno
▴ 100
0
votes
8
replies
1.6k
views
Thoughts on computer purchase
computer
written 18.1 years ago by
Lance Palmer
▴ 60
0
votes
9
replies
1.1k
views
Compare results from different analysis (Affymetrix)
updated 17.4 years ago by
Darlene Goldstein
▴ 230 • written 17.4 years ago by
Ingrid H. G. Østensen
▴ 700
0
votes
7
replies
758
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
11 weeks ago • updated 26 days ago
shepherl
3.9k
0
votes
8
replies
1.9k
views
error message in gcrma
cdf
affy
gcrma
matchprobes
plier
cdf
affy
gcrma
matchprobes
plier
updated 18.0 years ago by
Seth Falcon
★ 7.4k • written 18.0 years ago by
Mohammad Esad-Djou
▴ 520
0
votes
8
replies
2.0k
views
CRISPRseek: annotate gene
CRISPRseek
9.6 years ago • updated 9.0 years ago
Julie Zhu
★ 4.3k
0
votes
12
replies
2.2k
views
how deal with multiplicate affy probes?
mgu74av2
probe
affy
mgu74av2
probe
affy
updated 20.2 years ago by
Ron Ophir
▴ 80 • written 20.2 years ago by
Johnnidis, Jonathan
▴ 50
1
vote
14
replies
11k
views
Unable to connect from R 3.2.2
biocinstaller
source
8.5 years ago
michel.renou
• 0
0
votes
8
replies
2.1k
views
Gviz and AnnotateTrack and memory usage
gviz
updated 8.9 years ago by
florian.hahne@novartis.com
★ 1.6k • written 9.3 years ago by
Bogdan
▴ 670
3
votes
9
replies
5.1k
views
DESeq2 results with RUVSeq values
deseq2
ruvseq
sizefacotrs
updated 9.0 years ago by
davide risso
▴ 950 • written 9.0 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
7
replies
1.4k
views
how to split one word into letters
updated 19.5 years ago by
John Zhang
★ 2.9k • written 19.5 years ago by
Liu, Xin
▴ 130
1
vote
15
replies
3.3k
views
Issues with SGSeq: plotFeatures method returns NULL
sgseq
updated 7.6 years ago by
Leonard Goldstein
▴ 220 • written 7.8 years ago by
Sylvain Foisy
▴ 80
0
votes
13
replies
2.3k
views
alternate /tmp for Bioconductor install
updated 19.0 years ago by
Seth Falcon
★ 7.4k • written 19.0 years ago by
Robert Citek
▴ 120
1
vote
10
replies
2.2k
views
GEOquery
updated 15.8 years ago by
Sean Davis
21k • written 15.9 years ago by
Harpreet Saini
▴ 20
0
votes
8
replies
1.9k
views
getBioC problem
updated 18.3 years ago by
Seth Falcon
★ 7.4k • written 18.3 years ago by
Amy Mikhail
▴ 460
1
vote
9
replies
2.6k
views
RUV: removing unwanted variation in RNA-seq
RUV
ruvseq
rnaseq
9.0 years ago
sergio.espeso-gil
• 0
0
votes
13
replies
1.9k
views
Is a number within a set of ranges?
Cancer
Cancer
16.6 years ago
Daniel Brewer
★ 1.9k
0
votes
7
replies
2.0k
views
DiffBind:Treatments + second factor
DiffBind
diffbind
updated 9.5 years ago by
Rory Stark
★ 5.2k • written 9.5 years ago by
sergio.espeso-gil
• 0
2
votes
12
replies
2.3k
views
ann_objs$MAPCOUNTS <- AnnotationDbi:::createMAPCOUNTS(dbconn, prefix) does not work well
annotation
orgdb
8.3 years ago
knishida
▴ 20
0
votes
13
replies
2.8k
views
Sorting matrix by column
updated 11.6 years ago by
James W. MacDonald
65k • written 11.6 years ago by
Guest User
★ 13k
6
votes
14
replies
5.9k
views
GenomicAlignments is too slow with summarizeOverlaps
genomicalignments
RNASeq
genomicfeatures
summarizeoverlaps
updated 9.4 years ago by
Gordon Smyth
50k • written 9.4 years ago by
bioprog
• 0
4
votes
20
replies
2.5k
views
scaling loess curves
HiTC
gothic
diffhic
HiC
8.7 years ago
Bogdan
▴ 670
0
votes
9
replies
1.8k
views
(no subject)
limma
limma
updated 19.6 years ago by
Sailendra Gummadi
▴ 10 • written 19.6 years ago by
karen
▴ 30
0
votes
7
replies
2.0k
views
simpleaffy error
simpleaffy
simpleaffy
19.9 years ago
kfbargad@lg.ehu.es
▴ 260
8
votes
14
replies
3.8k
views
reactome.db is not updated?
genesetenrichment
pathways
reactome.db
updated 9.1 years ago by
willem.ligtenberg
▴ 150 • written 9.5 years ago by
Guangchuang Yu
★ 1.2k
0
votes
6
replies
1.3k
views
AnnBuilder failing Taffy examples
AnnBuilder
AnnBuilder
21.9 years ago
Barry Henderson
▴ 250
8
votes
14
replies
11k
views
Using msa msaPrettyPrint(): saving multiple alignement fasta file
msa
msaprettyprint()
fasta
updated 7.0 years ago by
tongtong.wang1210
• 0 • written 7.3 years ago by
Olorin
▴ 50
0
votes
7
replies
1.5k
views
[Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch function
Annotation
GO
BSgenome
BSgenome
ChIPpeakAnno
Annotation
GO
BSgenome
BSgenome
ChIPpeakAnno
updated 14.2 years ago by
Ivan Gregoretti
▴ 310 • written 14.2 years ago by
Julie Zhu
★ 4.3k
0
votes
6
replies
2.1k
views
spillover::flowCore problem: Error in match(unstained, sampleNames(x))
flowcore
spillover
flowcytometry
updated 6.3 years ago by
Samuel Ahuno
• 0 • written 8.2 years ago by
Daniel Prieto
• 0
3
votes
10
replies
4.5k
views
ChIPseeker question: enrichPeakOverlap to find enrichment of genomic annotations in peaks from GRanges
chipseeker
updated 8.6 years ago by
Guangchuang Yu
★ 1.2k • written 8.6 years ago by
francesca casalino
▴ 50
0
votes
7
replies
2.0k
views
analyzing HumanHT12 with lumi
Microarray
Normalization
probe
lumi
Microarray
Normalization
probe
lumi
updated 14.7 years ago by
die_stevie@web.de
▴ 50 • written 14.7 years ago by
Stefanie Figura
▴ 30
0
votes
9
replies
1.5k
views
Problem with ArrayQuality Package version 1.12
updated 16.9 years ago by
Paquet, Agnes
▴ 500 • written 16.9 years ago by
Peter White
▴ 80
0
votes
10
replies
2.5k
views
Protein/peptide mass
18.0 years ago
john seers IFR
▴ 810
0
votes
7
replies
1.9k
views
Limma and time-course data
limma
limma
updated 18.2 years ago by
Gordon Smyth
50k • written 18.2 years ago by
michael watson IAH-C
★ 3.4k
0
votes
8
replies
1.9k
views
Biological replication (was RNA degradation problem)
Normalization
probe
affy
affyPLM
Normalization
probe
affy
affyPLM
18.3 years ago
Naomi Altman
★ 6.0k
0
votes
7
replies
1.0k
views
Statistics for Diagnostic Microarrays
updated 19.9 years ago by
A.J. Rossini
▴ 810 • written 19.9 years ago by
michael watson IAH-C
★ 3.4k
0
votes
8
replies
2.0k
views
AnnBuilder and Kegg
Pathways
GO
Survival
Cancer
Organism
annotate
affydata
vsn
AnnBuilder
globaltest
GO
vsn
updated 17.5 years ago by
David Lapointe
▴ 190 • written 17.5 years ago by
John Zhang
★ 2.9k
0
votes
12
replies
1.9k
views
agi4x44kpreprocess package
updated 15.3 years ago by
Pedro López Romero
▴ 360 • written 15.3 years ago by
Erika Melissari
▴ 250
8
votes
16
replies
2.7k
views
Setting package name in makeTxDbPackage
genomicfeatures
txdb
updated 9.0 years ago by
Marc Carlson
★ 7.2k • written 9.0 years ago by
Diego Diez
▴ 760
5
votes
11
replies
2.1k
views
ChIPQC Error in .Call2 NCList object is too deep
ChIPQC
updated 6.5 years ago by
Thomas Carroll
▴ 420 • written 6.6 years ago by
Victor Goitea
▴ 10
2
votes
7
replies
2.7k
views
SomaticSignatures, cannot reproduce use case
somaticsignatures
'IRanges
9.6 years ago
Anna N.
• 0
5
votes
15
replies
2.7k
views
Rqc for RNA-Seq data
Rqc
8.3 years ago
kritikamish99
▴ 10
0
votes
6
replies
1.4k
views
Reading Imagene files with read.imagene in limma
updated 20.0 years ago by
Gordon Smyth
50k • written 20.0 years ago by
STKH Steen Krogsgaard
▴ 150
13
votes
21
replies
6.1k
views
modeling zero-dominated RNA-seq with voom/limma and hurdle models (pscl)
limma
voom
hurdle
single cell
8.7 years ago
osa.zuta
▴ 40
45,678 results • Page
2 of 914
Recent ...
Replies
Answer: ERROR; return code from pthread_create() is 22
by
James W. MacDonald
65k
Seems OK to me. ``` > dat <- ReadAffy() > dat AffyBatch object size of arrays=744x744 features (20 kb) cdf=HG-U219 (49386 affyids) …
Answer: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
65k
Unless you think the different lines or tissues will have very different within-group variances, you should just analyze together and make …
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
by
James W. MacDonald
65k
It appears that batch is orthogonal to the treatment, so you can just fit a batch effect in your model.
Answer: Control group between 2 batches have different expression in RNAseq data
by
James W. MacDonald
65k
Since batch is orthogonal to the treatment, you just add a batch factor to your model.
Answer: Subsetting RNAseq data | voomaByGroup()
by
Anna
• 0
Hi Gordon. Thank you so much. Your reply is extremely helpful, and I feel more confident moving forward with the analysis. Also, very inte…
Votes
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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