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replies
1.3k
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maQualityPlots: cannot coerce type 'S4' to vector of type
arrayQuality
arrayQualityMetrics
arrayQuality
arrayQualityMetrics
12.0 years ago
Agnes Paquet
▴ 30
0
votes
2
replies
1.2k
views
paCalls() in oligo package fails for exon arrays (Error in normalizeSingleBracketSubscript)
oligo
oligo
updated 12.0 years ago by
Benilton Carvalho
★ 4.3k • written 12.0 years ago by
Guest User
★ 13k
0
votes
3
replies
2.2k
views
Error reading imputed file using snpStats package
SNP
snpStats
SNP
snpStats
updated 12.0 years ago by
Vincent J. Carey, Jr.
6.7k • written 12.0 years ago by
francesca casalino
▴ 50
0
votes
0
replies
1.7k
views
Clusplot - changing cluster labels
12.0 years ago
lep
▴ 90
0
votes
6
replies
5.7k
views
Question about quantile normalization and NA value
Microarray
Normalization
limma
Microarray
Normalization
limma
updated 12.0 years ago by
godahajime
▴ 20 • written 12.0 years ago by
H@mamba.fhcrc.org
▴ 10
0
votes
0
replies
3.8k
views
maQualityPlots: cannot coerce type 'S4' to vector of type 'double'
arrayQuality
arrayQuality
12.0 years ago
Saket Choudhary
▴ 130
0
votes
1
reply
1.3k
views
Design matrix in Combat algorithm
sva
sva
updated 12.0 years ago by
W. Evan Johnson
▴ 870 • written 12.0 years ago by
Guest User
★ 13k
0
votes
0
replies
1.4k
views
rMAT install error
rMAT
rMAT
12.0 years ago
周在威
▴ 20
0
votes
7
replies
3.5k
views
[ReportingTools] and DESeq2 results, publish DESeqDataSet using resultsNames other than the default
Sequencing
ReportingTools
DESeq2
Sequencing
ReportingTools
DESeq2
updated 12.0 years ago by
James W. MacDonald
68k • written 12.0 years ago by
Dimitra Alexopoulou
▴ 30
0
votes
1
reply
1.1k
views
Get actual coordinates for the predicted loci
segmentSeq
segmentSeq
updated 12.0 years ago by
Thomas J Hardcastle
▴ 180 • written 12.0 years ago by
Guest User
★ 13k
0
votes
2
replies
2.5k
views
bsmooth and bsseq for RRBS
bsseq
bsseq
updated 12.0 years ago by
Tim Triche
★ 4.2k • written 12.0 years ago by
Guest User
★ 13k
0
votes
4
replies
1.7k
views
RRBS question
updated 12.0 years ago by
Tim Triche
★ 4.2k • written 12.0 years ago by
Alex Gutteridge
▴ 650
3
votes
2
replies
7.2k
views
get promoter regions (bed format) of genes hg19
IRanges
IRanges
updated 12.0 years ago by
Valerie Obenchain
★ 6.8k • written 12.0 years ago by
Guest User
★ 13k
0
votes
0
replies
1.4k
views
Summer Internship at Genentech
12.0 years ago
Jessica Larson
▴ 10
0
votes
0
replies
552
views
A relevant petition
12.0 years ago
Guest User
★ 13k
0
votes
0
replies
1.7k
views
ChIPpeakAnno: 6-way venn diagram
RNASeq
ChIPpeakAnno
RNASeq
ChIPpeakAnno
12.0 years ago
Julie Zhu
★ 4.3k
0
votes
3
replies
2.5k
views
how to extract probes for a probeset from PdInfo database?
miRNA
cdf
affy
miRNA
cdf
affy
updated 12.0 years ago by
Benilton Carvalho
★ 4.3k • written 12.0 years ago by
Guido Hooiveld
★ 4.1k
0
votes
1
reply
1.5k
views
FLowClust/FLowCore
graph
flowCore
graph
flowCore
updated 12.0 years ago by
Jiang, Mike
★ 1.3k • written 12.0 years ago by
Guest User
★ 13k
0
votes
6
replies
1.4k
views
Problem when trying to use \'affy\' package
Normalization
Normalization
updated 12.0 years ago by
James W. MacDonald
68k • written 12.0 years ago by
Guest User
★ 13k
1
vote
1
reply
6.9k
views
Voom and removing batch effect
Normalization
limma
Normalization
limma
updated 12.0 years ago by
Ryan C. Thompson
★ 7.9k • written 12.0 years ago by
Heather Estrella
▴ 30
0
votes
1
reply
1.5k
views
GOstats, query between the GO set from geneIdsByCategory and the GO set from org.Ce.egGO
GOstats
GOstats
updated 12.0 years ago by
Dan Du
▴ 210 • written 12.0 years ago by
余淼
▴ 10
0
votes
2
replies
3.9k
views
Problem installing BiocGenerics package
BiocGenerics
BiocGenerics
updated 12.0 years ago by
Dan Tenenbaum
★ 8.2k • written 12.0 years ago by
Guest User
★ 13k
1
vote
4
replies
5.1k
views
pre-ranked GSEA within R? + Best DESeq2/limma-voom metric?
DESeq2
12.0 years ago • updated 3.5 years ago
Gordon Smyth
53k
0
votes
2
replies
3.2k
views
Trouble installing BiocGenerics
BiocGenerics
BiocGenerics
12.0 years ago
Andreas Leha
▴ 30
0
votes
2
replies
1.7k
views
help with array based microRNA data analysis
limma
microRNA
limma
microRNA
updated 12.0 years ago by
Paul Geeleher
★ 1.3k • written 12.0 years ago by
Abhishek Pratap
▴ 190
0
votes
2
replies
985
views
conditional merge of duplicated rows in data.frame
updated 12.0 years ago by
Martin Morgan
25k • written 12.0 years ago by
Guest User
★ 13k
0
votes
0
replies
2.0k
views
pathview vectorized output?
Pathways
graph
pathview
Pathways
graph
pathview
12.0 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
937
views
IPPD model fit
PROcess
IPPD
PROcess
IPPD
12.0 years ago
Yuri Galachyants
▴ 10
0
votes
5
replies
1.5k
views
obtaining the counts after batch effect removal
updated 12.0 years ago by
Michael Love
43k • written 12.0 years ago by
Guest User
★ 13k
0
votes
0
replies
639
views
Problem with PMcorrection and Summarization
Normalization
Normalization
12.0 years ago
Guest User
★ 13k
0
votes
0
replies
3.6k
views
pre-ranked GSEA within R? + Best DESeq2/limma-voom
limma
edgeR
limma
edgeR
12.0 years ago
Gordon Smyth
53k
0
votes
4
replies
1.8k
views
Cluster stability/robustness
updated 12.0 years ago by
Wolfgang Huber
★ 13k • written 12.1 years ago by
Guest User
★ 13k
0
votes
1
reply
2.2k
views
fRMA for Gene ST arrays
Microarray
probe
oligo
frma
Microarray
probe
oligo
frma
updated 12.0 years ago by
Matthew McCall
▴ 830 • written 12.1 years ago by
maria
▴ 10
0
votes
1
reply
2.0k
views
Querying a HDF5 database from R
rhdf5
rhdf5
updated 12.0 years ago by
Bernd Fischer
▴ 550 • written 12.1 years ago by
Guest User
★ 13k
0
votes
9
replies
9.0k
views
DESeq2: NA on padj column when doing bonferroni
updated 12.1 years ago by
Kristina M Fontanez
▴ 220 • written 12.1 years ago by
David R
▴ 90
0
votes
0
replies
1.0k
views
tudelft.CytoscapeRPC.CytoscapeRPCCallHandler: width is too small
Network
Network
12.1 years ago
Paul Shannon
▴ 750
0
votes
0
replies
1.4k
views
RCytoscape: tudelft.CytoscapeRPC.CytoscapeRPCCallHandler: width is too small
SystemsBiology
Network
RCytoscape
SystemsBiology
Network
RCytoscape
12.1 years ago
Paul Shannon
▴ 750
0
votes
0
replies
2.0k
views
Labeling BAM files in Cufflinks/Cuffdiff input
12.1 years ago
Sindre
▴ 110
0
votes
8
replies
4.2k
views
Error installing development version of DESeq2
GUI
DESeq2
GUI
DESeq2
updated 12.1 years ago by
Dan Tenenbaum
★ 8.2k • written 12.0 years ago by
Kristina M Fontanez
▴ 220
0
votes
1
reply
1.0k
views
edgeR FC calculation question
updated 12.1 years ago by
Ryan C. Thompson
★ 7.9k • written 12.1 years ago by
Lana Schaffer
★ 1.3k
0
votes
4
replies
1.7k
views
finding a very large number of false positives using edgeR
Sequencing
RNASeq
edgeR
Sequencing
RNASeq
edgeR
updated 12.1 years ago by
Gordon Smyth
53k • written 12.1 years ago by
Blum, Charles
▴ 20
0
votes
18
replies
6.2k
views
DEseq2 metagenomic analysis without replicates
DESeq2
DESeq2
updated 12.1 years ago by
Kristina M Fontanez
▴ 220 • written 12.1 years ago by
Guest User
★ 13k
0
votes
2
replies
4.7k
views
ComBat: Error when including numerical covariates in model (numCovs)
sva
sva
updated 12.1 years ago by
Jordan Ramsey
▴ 20 • written 12.1 years ago by
W. Evan Johnson
▴ 870
0
votes
1
reply
1.4k
views
Inquiries on recommended design formulae for various experiments
DESeq2
DESeq2
updated 12.1 years ago by
Michael Love
43k • written 12.1 years ago by
Guest User
★ 13k
0
votes
0
replies
1.3k
views
ComBat: Error when including numerical covariates in model (numCovs)
sva
sva
12.1 years ago
Jordan Ramsey
▴ 20
0
votes
1
reply
2.2k
views
pathway analysis by SPIA using SPIA package vs graphite package
Pathways
SPIA
cycle
graphite
Pathways
SPIA
cycle
graphite
12.1 years ago
array chip
▴ 420
0
votes
9
replies
2.2k
views
DEXSeq - identical p-values for all exons in a gene
DEXSeq
DEXSeq
updated 12.1 years ago by
Steve Lianoglou
★ 13k • written 12.1 years ago by
Guest User
★ 13k
0
votes
1
reply
2.4k
views
makeTranscriptDbFromUCSC
TranscriptDb
TranscriptDb
12.1 years ago
Georg Otto
▴ 120
0
votes
3
replies
1.1k
views
makeGappedAlignmentPairs for broken pairs
updated 12.1 years ago by
Valerie Obenchain
★ 6.8k • written 12.1 years ago by
Ido M. Tamir
▴ 150
2
votes
2
replies
3.8k
views
biomaaRt error: Extra content at the end of the document
biomaRt
biomaRt
updated 12.1 years ago by
Steffen Durinck
▴ 540 • written 12.1 years ago by
Hari Easwaran
▴ 240
46,739 results • Page
512 of 935
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Comment: msmsTests, inconsistent sign between lFC.Av and LogFC
by
Ben
• 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis
by
James W. MacDonald
68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list'
by
varying.mastodon.isyn
• 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Comment: Confirm that OpenStats will not be archived (pryr dependency)
by
Marina
• 0
Thank you!
Comment: AnnotationForge makeOrgPackage rsqlite_send_query error
by
ansley.r.burtch
• 0
Hi! I am sure you are well into your career now and haven't worked on this for a while, but I wanted to let you know this is still helping …
Votes
Answer: How to directly decet the outlier samples (libraries) in EdgeR pipeline
Answer: Confused about the CPM and TMM normalization in edgeR
A: DESeq2 - VST eliminates zero values
Comment: Normalise to a housekeeping gene in DESEq2
Comment: limpa analysis advice
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