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edgeR- DE analysis with no replicates
edger
differential gene expression
without replicate
nested design
help
updated 7.8 years ago by
Aaron Lun
★ 28k • written 7.8 years ago by
knipehf
• 0
3
votes
4
replies
1.2k
views
why makeGRangesFromDataFrame don't do the IRange
HELP
HelloRanges
updated 18 months ago by
James W. MacDonald
65k • written 18 months ago by
michela
▴ 20
3
votes
4
replies
1.3k
views
GEO + RNA-seq. Total Newbie.
RNASeqData
RNASeq
GEO
RNASeqR
HELP
3.1 years ago
hgalmoore
• 0
2
votes
4
replies
1.7k
views
STRINGdb string_db$map error
STRINGdb
HELP
updated 14 months ago by
Rodrigo
▴ 10 • written 2.2 years ago by
Jessica
▴ 10
2
votes
6
replies
1.4k
views
Help me find the bug
DESeq2
HELP
14 months ago
Michael
• 0
1
vote
4
replies
5.9k
views
ClusterProfiler - How to : input file, groupGo, enrichGo
clusterprofiler
input files
error
help
updated 7.1 years ago by
Guangchuang Yu
★ 1.2k • written 7.1 years ago by
Mataivic
• 0
1
vote
9
replies
4.2k
views
DESeq problems
help
DESeq2
DESeqDataSetFromMatrix
rownames
updated 22 months ago by
Sanatan
• 0 • written 3.0 years ago by
dorina.jamniczky
• 0
1
vote
2
replies
2.4k
views
ChIPpeakAnno findOverlapsOfPeaks error: "Error in FUN(X[[i]], ...) : Inputs contains duplicated ranges. please recheck your inputs."
HELP
ChIPpeakAnno
2.5 years ago
lexi.kellington
• 0
0
votes
2
replies
1.3k
views
help me to analysis my data
limma
help
updated 8.4 years ago by
svlachavas
▴ 830 • written 8.4 years ago by
libya.tahani
• 0
0
votes
10
replies
1.5k
views
Peak annotation
HELP
ChIC.data
PeakDetection
ChipOnChipData
18 months ago
michela
▴ 20
0
votes
7
replies
1.8k
views
DESeq2 with interest only for 1 gene
R
deseq2
differential gene expression
help
7.9 years ago • updated 7.8 years ago
fischer87
• 0
0
votes
2
replies
1.0k
views
Design matrix choice for time series experiment using limma
limma
time series
help
updated 5.3 years ago by
Aaron Lun
★ 28k • written 5.3 years ago by
rm1238
• 0
0
votes
1
reply
2.0k
views
setup microbiome error
help
software error
updated 5.3 years ago by
Martin Morgan
25k • written 5.3 years ago by
mafusa20
• 0
0
votes
1
reply
323
views
Gene expression analysis and network construction for bachelor thesis
bachelorthesis
help
HELP
updated 8 months ago by
DrFizz
• 0 • written 8 months ago by
melander
• 0
0
votes
4
replies
1.2k
views
Volcano plot becomes flipped when I add a third condition
DESeq2
volcanoplot
deseq
HELP
contrast
updated 14 months ago by
Basti
▴ 780 • written 14 months ago by
Michael
• 0
0
votes
2
replies
713
views
Empty matrix
ChIPpeakAnno
Normalization
EnrichedHeatmap
HELP
TxDb.Celegans.UCSC.ce11.refGene
18 months ago
michela
▴ 20
0
votes
1
reply
566
views
Data visualization
HELP
Data
updated 20 months ago by
Guido Hooiveld
★ 3.9k • written 20 months ago by
mcclurejenniferc
• 0
17 results • Page
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Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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