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DEAnalysis
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2
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4
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Use of limma R package with targeted proteomics for DE analysis
DEanalysis
limma
olinktargetedproteomics
6 weeks ago • updated 4 weeks ago
svlachavas
▴ 840
3
votes
3
replies
2.9k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM
RNASeqData
DEAnalysis
limma
18 months ago
Ethan Nguyen
• 0
2
votes
10
replies
1.6k
views
How to get DE relative to a fold-change threshold in single factor experiments
edgeR
deanalysis
test fisher exact
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
thkapell
▴ 10
0
votes
0
replies
1.6k
views
Specific considerations in RNA-Seq DE analysis with edgeR pipeline for a TCGA dataset starting with HTSeq counts
edgeR
rnaseq
DEanalysis
TCGA
independent filtering
7.4 years ago
svlachavas
▴ 840
4 results • Page
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Comment: DESeq2 - human data, weird results, troubleshooting
by
bd2000
▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
James W. MacDonald
68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
ATpoint
★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt
by
darylruiz6545
• 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash
by
Alex
• 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Votes
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
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