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DESeq2 with GAGE
Pathways
cycle
gage
DESeq2
pathview
Pathways
cycle
gage
DESeq2
pathview
10.5 years ago
Luo Weijun
★ 1.6k
0
votes
1
reply
2.5k
views
SPIA error - Error in density.default(pfstmp, bw = sd(pfstmp)/4) : \'bw\' is not positive.
SPIA
cycle
SPIA
cycle
updated 10.4 years ago by
Tarca, Adi
▴ 570 • written 10.4 years ago by
Guest User
★ 13k
0
votes
3
replies
2.4k
views
Reading in data with HTqPCR
Cancer
cycle
Cancer
cycle
updated 13.9 years ago by
deepak roshan
▴ 40 • written 13.9 years ago by
Heidi Dvinge
★ 2.0k
0
votes
1
reply
1.9k
views
FW: URGENT Help required: Getting this error with GAGE analysis, input files attached
Microarray
Annotation
Pathways
GO
Cancer
Breast
cycle
gage
Microarray
Annotation
GO
updated 12.3 years ago by
Javerjung Sandhu
▴ 200 • written 12.3 years ago by
Martin Morgan
25k
0
votes
3
replies
1.9k
views
runSPIA() in graphite package
Pathways
Breast
siggenes
PROcess
cycle
graphite
Pathways
Breast
siggenes
PROcess
cycle
updated 11.2 years ago by
Enrica
▴ 20 • written 11.2 years ago by
array chip
▴ 420
0
votes
0
replies
1.9k
views
How to do GO enrichment analysis with GOstats while the gene set with no p values of gene difference expression
Transcription
PROcess
GOstats
cycle
Transcription
PROcess
GOstats
cycle
13.7 years ago
zhidong yuan
▴ 10
0
votes
3
replies
1.8k
views
ReportingTools and gene annotation
Annotation
GO
cycle
ReportingTools
DESeq2
Annotation
GO
cycle
ReportingTools
DESeq2
updated 10.2 years ago by
James W. MacDonald
65k • written 10.2 years ago by
Ugo Borello
▴ 340
0
votes
3
replies
1.8k
views
pathway ID in KEGG.db
Pathways
cycle
Pathways
cycle
updated 11.8 years ago by
Marc Carlson
★ 7.2k • written 11.8 years ago by
Ed
▴ 230
0
votes
0
replies
1.7k
views
getGEO problem
aCGH
gpls
aCGH
GEOquery
cycle
aCGH
gpls
aCGH
GEOquery
cycle
14.2 years ago
Sean Davis
21k
0
votes
8
replies
1.7k
views
Filtering BAM files by start position for VariantTools
Coverage
Cancer
cycle
VariantTools
Coverage
Cancer
cycle
VariantTools
updated 10.7 years ago by
Taylor, Sean D
▴ 250 • written 10.7 years ago by
Martin Morgan
25k
0
votes
1
reply
1.7k
views
pathway analysis by SPIA using SPIA package vs graphite package
Pathways
SPIA
cycle
graphite
Pathways
SPIA
cycle
graphite
10.3 years ago
array chip
▴ 420
0
votes
0
replies
1.6k
views
Cell cycle analysis of FACS data
rflowcyt
cycle
rflowcyt
cycle
17.8 years ago
Ulrik Stervbo
▴ 80
0
votes
0
replies
1.6k
views
qPCR event preview - April 2010
miRNA
qPCR
Normalization
probe
microRNA
cycle
miRNA
qPCR
Normalization
probe
microRNA
14.0 years ago
qPCR Platform - the reference in real-t…
▴ 170
0
votes
4
replies
1.5k
views
Reading in data with HTqPCR
qPCR
Cancer
cycle
HTqPCR
qPCR
Cancer
cycle
HTqPCR
13.9 years ago
Heidi Dvinge
★ 2.0k
0
votes
1
reply
1.4k
views
TLDA data
Clustering
Cancer
PROcess
cycle
HTqPCR
Clustering
Cancer
PROcess
cycle
HTqPCR
updated 13.9 years ago by
Heidi Dvinge
★ 2.0k • written 13.9 years ago by
deepak roshan
▴ 40
0
votes
4
replies
1.4k
views
Anyone have a GO slim list for Affy HG-U133A or HG-U133Av2?
Annotation
GO
annotate
affy
PROcess
Category
cycle
Annotation
GO
annotate
affy
PROcess
updated 19.2 years ago by
Aedin Culhane
▴ 310 • written 19.2 years ago by
Ken Termiso
▴ 250
0
votes
3
replies
1.4k
views
paired sample LIMMA
limma
cycle
limma
cycle
updated 12.9 years ago by
Achilleas Pitsillides
▴ 170 • written 12.9 years ago by
elliot harrison
▴ 230
0
votes
1
reply
1.3k
views
CRAN packages maintained by you
hexbin
gpls
RBGL
impute
Icens
hopach
maanova
RLMM
CORREP
cycle
hexbin
gpls
RBGL
Icens
updated 12.5 years ago by
Nicholas Lewin-Koh
▴ 430 • written 12.5 years ago by
Kurt Hornik
▴ 10
0
votes
0
replies
1.3k
views
structure of cfx file for HTqPCR
Microarray
qPCR
cycle
HTqPCR
Microarray
qPCR
cycle
HTqPCR
11.2 years ago
Guest User
★ 13k
0
votes
4
replies
1.3k
views
Accessing old versions of bioc packages
cycle
cycle
updated 11.0 years ago by
Dan Tenenbaum
★ 8.2k • written 11.0 years ago by
Julian Gehring
★ 1.3k
0
votes
1
reply
1.3k
views
Request for the assistance to use MEDME
Microarray
Normalization
Organism
probe
limma
MEDME
cycle
ASSIGN
Microarray
Normalization
updated 15.3 years ago by
Mattia Pelizzola
▴ 30 • written 15.3 years ago by
Prashantha Hebbar Kiradi [MU-MLSC]
▴ 90
0
votes
0
replies
1.3k
views
JOB: Microarray Bioinformatics Specialist
Microarray
Cancer
CGH
cycle
Microarray
Cancer
CGH
cycle
16.2 years ago
Robert Castelo
★ 3.3k
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
1.2k
views
affy : ReadAffy() fails on HuGene-1_1-st-v1 chips
Microarray
cdf
affy
makecdfenv
PROcess
oligo
cycle
Microarray
cdf
affy
makecdfenv
oligo
updated 12.2 years ago by
James W. MacDonald
65k • written 12.2 years ago by
Groot, Philip de
▴ 630
0
votes
2
replies
1.2k
views
reviews for quality control
cycle
cycle
updated 11.7 years ago by
Paul Geeleher
★ 1.3k • written 11.7 years ago by
carol white
▴ 680
0
votes
2
replies
1.2k
views
Finding coding SNPs with predictCoding
SNP
Annotation
BSgenome
ctc
BSgenome
cycle
genomes
SNP
Annotation
BSgenome
ctc
BSgenome
updated 12.1 years ago by
Thomas Girke
★ 1.7k • written 12.1 years ago by
Valerie Obenchain
★ 6.8k
0
votes
0
replies
1.2k
views
how to combine microarray data and phenotype data into a least squares analysis?
Microarray
cycle
Microarray
cycle
15.6 years ago
Amy Mikhail
▴ 460
0
votes
2
replies
1.2k
views
how to combine microarray data and phenotype data into a least squares analysis?
Microarray
cycle
Microarray
cycle
updated 15.6 years ago by
James W. MacDonald
65k • written 15.6 years ago by
Martin Bonke
▴ 40
0
votes
1
reply
1.1k
views
how does ShortRead function identify score system
cycle
cycle
updated 11.6 years ago by
Martin Morgan
25k • written 11.6 years ago by
wang peter
★ 2.0k
0
votes
1
reply
1.1k
views
FW: Request for the assistance to use MEDME
Normalization
Organism
probe
MEDME
cycle
ASSIGN
Normalization
Organism
probe
MEDME
cycle
updated 15.4 years ago by
Mattia Pelizzola
▴ 30 • written 15.4 years ago by
Prashantha Hebbar Kiradi [MU-MLSC]
▴ 90
0
votes
3
replies
1.0k
views
ShortRead Per Cycle Score
GO
cycle
GO
cycle
updated 14.0 years ago by
Martin Morgan
25k • written 14.0 years ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
1.0k
views
Cho et al.'s Expression Dataset in Yeast
Yeast
cycle
Yeast
cycle
updated 19.0 years ago by
xpeng
▴ 60 • written 19.0 years ago by
Ho-Joon Lee
▴ 20
0
votes
0
replies
1.0k
views
Subsetting vcf file by subject
VariantAnnotation
Annotation
cycle
VariantAnnotation
VariantAnnotation
Annotation
cycle
11.0 years ago
Valerie Obenchain
★ 6.8k
0
votes
1
reply
1.0k
views
sir
Cancer
cycle
HTqPCR
Cancer
cycle
HTqPCR
updated 13.9 years ago by
deepak roshan
▴ 40 • written 14.0 years ago by
Heidi Dvinge
★ 2.0k
0
votes
2
replies
993
views
some basic questions
Microarray
Annotation
Normalization
cdf
probe
cycle
Microarray
Annotation
Normalization
updated 12.4 years ago by
Richard Friedman
★ 2.0k • written 12.4 years ago by
anand m t
▴ 40
0
votes
0
replies
983
views
replicable of *PLGEM*
plgem
cycle
plgem
cycle
13.6 years ago
Pavelka, Norman
▴ 70
0
votes
0
replies
979
views
Biostrings
GO
Cancer
Biostrings
cycle
GO
Cancer
Biostrings
cycle
11.2 years ago
Hervé Pagès
16k
0
votes
0
replies
967
views
Differentially Expressed Genes in Time Series with Replications
Yeast
cycle
Yeast
cycle
17.3 years ago
peter robinson
▴ 300
0
votes
1
reply
956
views
affy 1 cycle vs 2 cycle labeling kit
cycle
cycle
updated 19.9 years ago by
Michael Seewald
▴ 130 • written 19.9 years ago by
YUK FAI LEUNG
▴ 140
0
votes
2
replies
931
views
some basic questions
Microarray
Normalization
cdf
cycle
Microarray
Normalization
cdf
cycle
updated 12.4 years ago by
Sean Davis
21k • written 12.4 years ago by
Guest User
★ 13k
0
votes
1
reply
915
views
Finding coding SNPs with predictCoding
SNP
Annotation
BSgenome
BSgenome
GenomicFeatures
cycle
genomes
SNP
Annotation
BSgenome
updated 12.0 years ago by
Thomas Girke
★ 1.7k • written 12.0 years ago by
Valerie Obenchain
★ 6.8k
0
votes
0
replies
884
views
RMA verse GCRMA, low intensity
cycle
cycle
19.1 years ago
Matthew Hannah
▴ 940
0
votes
0
replies
878
views
major alterations to GGdata/GGtools planned
SNP
snpMatrix
cycle
SNP
snpMatrix
cycle
16.1 years ago
Vincent J. Carey, Jr.
6.7k
0
votes
0
replies
858
views
Using different file formats with oligo and analysis packages using oligo
SNP
Microarray
qPCR
cycle
SNP
Microarray
qPCR
cycle
11.3 years ago
Hans Thompson
▴ 30
0
votes
0
replies
853
views
Fwd: Unable to install packages
Microarray
Annotation
cdf
probe
cycle
Microarray
Annotation
cdf
probe
cycle
12.8 years ago
James W. MacDonald
65k
0
votes
2
replies
822
views
about plot rglist
Microarray
Cancer
limma
cycle
Microarray
Cancer
limma
cycle
updated 17.6 years ago by
Jenny Drnevich
★ 2.2k • written 17.6 years ago by
James W. MacDonald
65k
0
votes
0
replies
816
views
Re: webbioc and multtest
webbioc
cycle
webbioc
cycle
20.4 years ago
Colin A. Smith
▴ 220
0
votes
0
replies
810
views
Release 1.1
cycle
cycle
21.5 years ago
Jeff Gentry
★ 3.9k
0
votes
0
replies
758
views
New release of triplex package
cycle
cycle
10.5 years ago
Jiří Hon
▴ 20
0
votes
0
replies
741
views
LIMMA
limma
cycle
limma
cycle
18.2 years ago
Gordon Smyth
50k
50 results • Page
1 of 1
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Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
shuwangxinze1996
• 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough? Thank …
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A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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