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assign
•
reset
1
vote
3
replies
1.3k
views
Limma and Names Assignment
ASSIGN
ASSIGN
written 12.6 years ago by
Voke AO
▴ 760
0
votes
0
replies
633
views
Error in data.frame(ASSIGN = "ASSIGN parameters", version = as.character(utils::packageVersion("ASSIGN")), : arguments imply differing number of …
software error
assign
3.8 years ago
yueli7
▴ 20
0
votes
2
replies
1.1k
views
LIMMA: how to assign file name
limma
ASSIGN
limma
ASSIGN
updated 5.3 years ago by
Bioconductor Community
0 • written 19.0 years ago by
Guoneng Zhong
▴ 180
0
votes
11
replies
3.5k
views
SNP6 data to VCF
SNP
oligo
ASSIGN
SNP
oligo
ASSIGN
updated 5.7 years ago by
giulio.genovese
• 0 • written 12.2 years ago by
Sean Davis
21k
0
votes
1
reply
990
views
Query regarding DESeq
DESeq
ASSIGN
DESeq
ASSIGN
updated 9.8 years ago by
Wolfgang Huber
★ 13k • written 9.8 years ago by
Gourja Bansal
▴ 10
0
votes
5
replies
4.3k
views
annotating microarray data with mogene10stv1
Microarray
Annotation
annotate
limma
ASSIGN
Microarray
Annotation
annotate
limma
ASSIGN
updated 9.8 years ago by
James W. MacDonald
65k • written 9.8 years ago by
Jakub Stanislaw Nowak
▴ 70
0
votes
8
replies
3.1k
views
Annotation files for bacterial genome RNAseq
Alignment
Annotation
ASSIGN
Alignment
Annotation
ASSIGN
updated 9.9 years ago by
James W. MacDonald
65k • written 9.9 years ago by
José Luis Lavín
▴ 80
0
votes
2
replies
1.2k
views
error on detecting regions
ASSIGN
ASSIGN
updated 9.9 years ago by
Pan Du
▴ 440 • written 9.9 years ago by
Guest User
★ 13k
0
votes
4
replies
1.5k
views
GenomicRanges select parameter
GenomicRanges
ASSIGN
GenomicRanges
ASSIGN
updated 9.9 years ago by
Karolis Uziela
▴ 30 • written 9.9 years ago by
Michael Lawrence
★ 11k
0
votes
1
reply
2.5k
views
DataFrame(..., check.names=F); colnames change when assign data using '[[', not when using '[,]'
ASSIGN
ASSIGN
updated 9.9 years ago by
Michael Lawrence
★ 11k • written 9.9 years ago by
Ludo Pagie
▴ 40
0
votes
3
replies
1.2k
views
Dealing with probes with high fold change but PA call 0
Clustering
probe
ASSIGN
Clustering
probe
ASSIGN
updated 10.4 years ago by
Steve Lianoglou
★ 13k • written 10.4 years ago by
Gundala Viswanath
▴ 230
0
votes
5
replies
2.2k
views
Single-channel GenePix analysis with Limma (bg correction, normalization, weights)
Microarray
Normalization
vsn
limma
ASSIGN
Microarray
Normalization
vsn
limma
ASSIGN
updated 10.5 years ago by
Gordon Smyth
50k • written 10.5 years ago by
Marcin Jakub Kamiński
▴ 40
0
votes
1
reply
1.3k
views
ChIPpeakAnno
ChIPpeakAnno
ASSIGN
ChIPpeakAnno
ASSIGN
10.9 years ago
Julie Zhu
★ 4.3k
0
votes
2
replies
3.6k
views
From location to get the SNP rs ID
SNP
Cancer
SNPlocs
ASSIGN
SNP
Cancer
SNPlocs
ASSIGN
updated 10.9 years ago by
Hervé Pagès
16k • written 10.9 years ago by
Fabrice Tourre
▴ 970
0
votes
1
reply
1.7k
views
Fwd: feature weights in 'superpc' package
Survival
ASSIGN
Survival
ASSIGN
updated 11.0 years ago by
Tim Triche
★ 4.2k • written 11.0 years ago by
Yukti Choudhury
▴ 10
0
votes
5
replies
1.9k
views
Question regarding cellhts2 output
Normalization
Visualization
PROcess
cellHTS2
ASSIGN
Normalization
Visualization
PROcess
11.1 years ago
maziz@tgen.org
▴ 70
0
votes
1
reply
1.1k
views
fRMA for Gene ST arrays
affy
oligo
frma
ASSIGN
affy
oligo
frma
ASSIGN
updated 11.1 years ago by
Matthew McCall
▴ 830 • written 11.1 years ago by
Kamila Naxerova
▴ 100
0
votes
0
replies
1.1k
views
how to use color to represent significant changed genes in maPlot of edgeR
ASSIGN
ASSIGN
11.1 years ago
wang peter
★ 2.0k
0
votes
5
replies
2.2k
views
yieldSize and paired end data in SummarizeOverlaps error?
BSgenome
PROcess
BSgenome
ASSIGN
BSgenome
PROcess
BSgenome
ASSIGN
updated 11.2 years ago by
Valerie Obenchain
★ 6.8k • written 11.2 years ago by
Thomas Whisenant
▴ 10
0
votes
0
replies
837
views
Finding genes with minimal expression across a set of conditions?
ASSIGN
ASSIGN
11.2 years ago
Ryan C. Thompson
★ 7.9k
0
votes
0
replies
1.5k
views
Classification in Mass Spectrometry Data
Microarray
Classification
Cancer
Ovarian
PROcess
MLInterfaces
ASSIGN
Microarray
Cancer
11.5 years ago
McGee, Monnie
▴ 300
0
votes
2
replies
1.4k
views
Question regarding cellhts2 output
Normalization
cellHTS2
ASSIGN
Normalization
cellHTS2
ASSIGN
11.8 years ago
maziz@tgen.org
▴ 70
0
votes
12
replies
2.1k
views
Newbie methylation and stats question
probe
ASSIGN
probe
ASSIGN
updated 11.9 years ago by
Tim Triche
★ 4.2k • written 11.9 years ago by
Gustavo Fernández Bayón
▴ 440
0
votes
0
replies
2.7k
views
qrqc with error message of "unable to start device PNG" and "unable to open connection to X11 display"?
GO
qrqc
ASSIGN
GO
qrqc
ASSIGN
11.9 years ago
Sang Chul Choi
▴ 230
0
votes
4
replies
1.5k
views
edgeR: design matrix
ASSIGN
ASSIGN
updated 11.9 years ago by
Gordon Smyth
50k • written 12.0 years ago by
KJ Lim
▴ 420
0
votes
4
replies
3.5k
views
edgeR : input and design matrix help
edgeR
ASSIGN
edgeR
ASSIGN
12.0 years ago
KJ Lim
▴ 420
0
votes
0
replies
1.1k
views
edgeR input and design matrix help
edgeR
ASSIGN
edgeR
ASSIGN
12.0 years ago
KJ Lim
▴ 420
0
votes
0
replies
1.0k
views
problems with oneChannelGUI
affylmGUI
oneChannelGUI
ASSIGN
affylmGUI
oneChannelGUI
ASSIGN
12.1 years ago
Manuela Di Russo
▴ 70
0
votes
1
reply
918
views
RangedData Element Metadata
Coverage
rtracklayer
ASSIGN
Coverage
rtracklayer
ASSIGN
updated 12.1 years ago by
Michael Lawrence
★ 11k • written 12.1 years ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
955
views
Creating a customized cut flow with the affy/limma packages
GO
limma
ASSIGN
GO
limma
ASSIGN
updated 12.2 years ago by
James W. MacDonald
65k • written 12.2 years ago by
J.M.Jensen
▴ 20
0
votes
1
reply
974
views
Creating a customized cut flow with the affy/limma packages
GO
hgu133plus2
limma
ASSIGN
GO
hgu133plus2
limma
ASSIGN
updated 12.2 years ago by
James W. MacDonald
65k • written 12.2 years ago by
Guest User
★ 13k
0
votes
2
replies
1.2k
views
DEseq
ASSIGN
ASSIGN
updated 12.2 years ago by
Naomi Altman
★ 6.0k • written 12.3 years ago by
saikouy bah
▴ 30
0
votes
4
replies
1.5k
views
problem in reading bam files with EDASeq
Rsamtools
EDASeq
ASSIGN
Rsamtools
EDASeq
ASSIGN
updated 12.3 years ago by
davide risso
▴ 950 • written 12.3 years ago by
rcaloger
▴ 500
0
votes
2
replies
1.2k
views
htSeqTools - naming RangedData objects?
htSeqTools
ASSIGN
htSeqTools
ASSIGN
updated 12.3 years ago by
Michael Lawrence
★ 11k • written 12.3 years ago by
Ian D.
▴ 70
0
votes
0
replies
1.4k
views
limma - 2-color agilent microarray, GO annotation
Microarray
Annotation
GO
Organism
limma
GOstats
oligo
ASSIGN
Microarray
Annotation
GO
12.3 years ago
Gordon Smyth
50k
0
votes
1
reply
1.1k
views
goSeq error
Cancer
PROcess
edgeR
goseq
ASSIGN
Cancer
PROcess
edgeR
goseq
ASSIGN
12.5 years ago
Matthew Young
▴ 50
0
votes
0
replies
1.4k
views
illuminaHumanv4 mappings
Infrastructure
Cancer
Homo sapiens
probe
AnnotationDbi
ASSIGN
Infrastructure
Cancer
probe
12.6 years ago
Mark Cowley
▴ 910
0
votes
0
replies
844
views
"timecourse" package, problem with ordering of samples.
ASSIGN
ASSIGN
12.6 years ago
dha 2001
▴ 30
0
votes
0
replies
1.2k
views
doubt in HTqPCR
Cancer
ddCt
cycle
HTqPCR
ASSIGN
Cancer
ddCt
cycle
HTqPCR
ASSIGN
12.6 years ago
Heidi Dvinge
★ 2.0k
0
votes
2
replies
1.6k
views
plotting probes along a chromosome
graph
GenomeGraphs
ASSIGN
graph
GenomeGraphs
ASSIGN
updated 12.8 years ago by
Oosting, J. PATH
▴ 550 • written 12.8 years ago by
Pete Shepard
▴ 240
0
votes
1
reply
4.2k
views
simpleafy plots
ASSIGN
ASSIGN
updated 13.1 years ago by
James W. MacDonald
65k • written 13.1 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
1
reply
925
views
Using Sample IDs from Sample Name column
ASSIGN
ASSIGN
updated 13.1 years ago by
Heidi Dvinge
★ 2.0k • written 13.1 years ago by
Ross Haggart
▴ 10
0
votes
3
replies
1.3k
views
working with two factors in DESeq to analyze RNA-seq
DESeq
ASSIGN
DESeq
ASSIGN
updated 13.2 years ago by
Gordon Smyth
50k • written 13.2 years ago by
Biase, Fernando
▴ 150
0
votes
1
reply
1.0k
views
question about get a summary gene expression information from the probe set associated with one specific gene
Annotation
GO
cdf
probe
affy
convert
ASSIGN
Annotation
GO
cdf
probe
affy
convert
updated 13.3 years ago by
Xiaowei Guan
▴ 90 • written 13.3 years ago by
James W. MacDonald
65k
0
votes
0
replies
924
views
question about get a summary gene expression information from the probe set associated with one specific gene
Annotation
probe
convert
ASSIGN
Annotation
probe
convert
ASSIGN
13.4 years ago
Xiaowei Guan
▴ 90
0
votes
9
replies
2.8k
views
Conversion of affymetrix cell file to raw text file
Microarray
probe
ASSIGN
Microarray
probe
ASSIGN
13.4 years ago
viritha kaza
▴ 580
0
votes
3
replies
1.3k
views
Question about clustering and cluster validation
ASSIGN
ASSIGN
updated 13.5 years ago by
Robert Chapman
▴ 20 • written 13.5 years ago by
January Weiner
▴ 370
0
votes
8
replies
2.9k
views
biomaRt - batch query for chromosome location to gene identifier?
biomaRt
ASSIGN
biomaRt
ASSIGN
updated 13.5 years ago by
Vincent J. Carey, Jr.
6.7k • written 13.5 years ago by
Kemal Akat
▴ 120
0
votes
1
reply
1.3k
views
Bootstrapping paired samples and tiny groups
ASSIGN
ASSIGN
updated 13.6 years ago by
Naomi Altman
★ 6.0k • written 13.7 years ago by
Benjamin Otto
▴ 830
0
votes
2
replies
1.3k
views
error/problem with biomaRt gene symbol query
Microarray
Cancer
probe
biomaRt
ASSIGN
Microarray
Cancer
probe
biomaRt
ASSIGN
updated 13.8 years ago by
Steffen
▴ 500 • written 13.8 years ago by
Sergii Ivakhno
▴ 100
50 results • Page
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Replies
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Intent to delete when going home. Sorry for that!
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
Please ask you own question. Inserting your own dataset into someone else's question like this is very impolite. I have already answered m…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Thanks Gordon for the advice!
Votes
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
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