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Showing :
expression
•
reset
5
votes
8
replies
1.9k
views
Question on performing filtering by gene expression on a normalized matrix in limma?
expression
R
filtering
limma
19 months ago • updated 16 months ago
mohammedtoufiq91
▴ 10
0
votes
0
replies
443
views
Argument is of length zero in variancePartition/Dream
expression
variancePartition
edgeR
20 months ago
Jonathan
• 0
0
votes
1
reply
1.1k
views
Re-normalize microarray dataset in R
microarray
quantile
expression
R
Normalization
updated 2.8 years ago by
Konstantinos Yeles
▴ 80 • written 2.8 years ago by
mohammedtoufiq91
▴ 10
1
vote
1
reply
1.1k
views
Table expression data from GEO file
GEO
expression
GEOquery
updated 4.0 years ago by
Robert Castelo
★ 3.3k • written 4.0 years ago by
lsbew
• 0
1
vote
9
replies
1.9k
views
Difference between gene-level test and transcript-level test with RATs (Relative Abundance of Transcrits)
RATs
RNA-Seq
Isoforms
DTU
expression
updated 4.8 years ago by
fruce_ki
▴ 20 • written 4.8 years ago by
UserAnonyme
• 0
1
vote
2
replies
693
views
Two factors design with DESEq2
deseq2
genes
expression
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
UserAnonyme
• 0
7
votes
3
replies
3.2k
views
Log2(RPKM) counts in Bioconductor
rpkm
scater
calcaverage
R
expression
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
kushshah
▴ 10
0
votes
6
replies
1.3k
views
variancePartition - testing for individuals
variance
formula
expression
updated 5.3 years ago by
mikhael.manurung
▴ 270 • written 5.3 years ago by
rina
▴ 30
0
votes
0
replies
1.6k
views
Job:
Research Associate, Cambridge, UK - Oesophageal Cancer ICGC project
job
sequencing
methylation
expression
Job
9.2 years ago
Andy Lynch
▴ 120
6
votes
5
replies
1.8k
views
Limma ebayes returns a list with Affy pd.hugene.2.0.st arrays
ebayes
expression
affymetrix
pd.hugene.2.0.st
limma
updated 9.3 years ago by
Gordon Smyth
50k • written 9.3 years ago by
Paulo Nuin
▴ 200
10 results • Page
1 of 1
Recent ...
Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
Awards
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to
Gordon Smyth
50k
Popular Question
to
Chris
• 0
Supporter
to
Jonathan
▴ 10
Popular Question
to
Bine
▴ 40
Scholar
to
ATpoint
★ 4.0k
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