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Bioconductor unable to update 'curl'
curl
HELP
9 months ago
kagodwi2
• 0
0
votes
2
replies
962
views
iam not able to do retrive data using GEOquery R package
HELP
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
ramya20kumar20
• 0
0
votes
9
replies
2.4k
views
'path' must be string
HELP
path
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
cpierce2
• 0
0
votes
1
reply
809
views
Gene expression analysis and network construction for bachelor thesis
bachelorthesis
help
HELP
updated 2.4 years ago by
DrFizz
• 0 • written 2.5 years ago by
melander
• 0
2
votes
6
replies
2.7k
views
Help me find the bug
DESeq2
HELP
2.9 years ago
Michael
• 0
0
votes
4
replies
2.7k
views
Volcano plot becomes flipped when I add a third condition
DESeq2
volcanoplot
deseq
HELP
contrast
updated 2.9 years ago by
Basti
▴ 780 • written 2.9 years ago by
Michael
• 0
0
votes
2
replies
1.2k
views
Empty matrix
ChIPpeakAnno
Normalization
EnrichedHeatmap
HELP
TxDb.Celegans.UCSC.ce11.refGene
3.3 years ago • updated 3.2 years ago
michela
▴ 20
3
votes
4
replies
1.9k
views
why makeGRangesFromDataFrame don't do the IRange
HELP
HelloRanges
updated 3.2 years ago by
James W. MacDonald
68k • written 3.3 years ago by
michela
▴ 20
0
votes
10
replies
2.7k
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Peak annotation
HELP
ChIC.data
PeakDetection
ChipOnChipData
3.3 years ago
michela
▴ 20
0
votes
1
reply
1.1k
views
Data visualization
HELP
Data
updated 3.4 years ago by
Guido Hooiveld
★ 4.1k • written 3.4 years ago by
mcclurejenniferc
• 0
2
votes
4
replies
3.2k
views
STRINGdb string_db$map error
STRINGdb
HELP
updated 2.9 years ago by
Rodrigo
▴ 10 • written 3.9 years ago by
Jessica
▴ 10
1
vote
2
replies
3.6k
views
ChIPpeakAnno findOverlapsOfPeaks error: "Error in FUN(X[[i]], ...) : Inputs contains duplicated ranges. please recheck your inputs."
HELP
ChIPpeakAnno
4.2 years ago
lexi.kellington
• 0
1
vote
9
replies
7.4k
views
DESeq problems
help
DESeq2
DESeqDataSetFromMatrix
rownames
updated 3.6 years ago by
Sanatan
• 0 • written 4.8 years ago by
dorina.jamniczky
• 0
3
votes
4
replies
2.3k
views
GEO + RNA-seq. Total Newbie.
RNASeqData
RNASeq
GEO
RNASeqR
HELP
4.8 years ago
hgalmoore
• 0
0
votes
1
reply
2.7k
views
setup microbiome error
help
software error
updated 7.0 years ago by
Martin Morgan
25k • written 7.0 years ago by
mafusa20
• 0
0
votes
2
replies
1.5k
views
Design matrix choice for time series experiment using limma
limma
time series
help
updated 7.0 years ago by
Aaron Lun
★ 29k • written 7.0 years ago by
rm1238
• 0
1
vote
4
replies
8.1k
views
ClusterProfiler - How to : input file, groupGo, enrichGo
clusterprofiler
input files
error
help
updated 8.9 years ago by
Guangchuang Yu
★ 1.2k • written 8.9 years ago by
Mataivic
• 0
4
votes
5
replies
3.1k
views
edgeR- DE analysis with no replicates
edger
differential gene expression
without replicate
nested design
help
updated 9.6 years ago by
Aaron Lun
★ 29k • written 9.6 years ago by
knipehf
• 0
0
votes
7
replies
2.7k
views
DESeq2 with interest only for 1 gene
R
deseq2
differential gene expression
help
9.6 years ago
fischer87
• 0
0
votes
2
replies
1.8k
views
help me to analysis my data
limma
help
updated 10.2 years ago by
svlachavas
▴ 840 • written 10.2 years ago by
libya.tahani
• 0
20 results • Page
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
ja569116
• 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice
by
Gordon Smyth
53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma
by
Gordon Smyth
53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
I updated the above answer today.
Answer: When to use edgeR or limma
by
James W. MacDonald
68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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