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Showing :
ebayes
•
reset
5
votes
4
replies
485
views
Limma outputs different results for same sample?
topTable
MicroarrayData
ebayes
limma
Microarray
15 months ago
snijesh
▴ 20
0
votes
5
replies
381
views
eBayes options and decideTests method
limma
eBayes
decideTests
topTable
updated 2.2 years ago by
Gordon Smyth
45k • written 2.2 years ago by
irene.roman
• 0
0
votes
6
replies
592
views
eBayes(fit_object, trend = T) gives: Error in fitFDist(var, df1 = df, covariate = covariate) : NA covariate values not allowed
limma
eBayes
updated 3.2 years ago by
Gordon Smyth
45k • written 3.2 years ago by
Sebastian Hesse
▴ 60
3
votes
1
reply
622
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma
ebayes
bayesian
ls
updated 3.6 years ago by
Gordon Smyth
45k • written 3.6 years ago by
CantExitVIM
▴ 10
1
vote
7
replies
828
views
model.matrix from GDS data
model.matrix
lmFit
eBayes
GEOquery
limma
4.2 years ago
darthratus
• 0
1
vote
2
replies
873
views
Limma Ebayes on SILAC data
ebayes
limma
bioconductor
updated 4.5 years ago by
Gordon Smyth
45k • written 4.5 years ago by
reventropy2003
▴ 10
0
votes
6
replies
1.3k
views
Error in last step of Limma analysis (eBayes)
ebayes
limma
4.6 years ago
peirinl
• 0
1
vote
3
replies
1.1k
views
Error from eBayes in limma package
eBayes
limma
error
updated 4.8 years ago by
James W. MacDonald
59k • written 4.8 years ago by
calen.p.ryan
• 0
2
votes
2
replies
978
views
Can one get LSMeans and expression confidence intervals from limma and voom?
ebayes
limma
voom
5.2 years ago
bag59
• 0
1
vote
2
replies
1.2k
views
error in Limma analysis - estimated df (df.0) for prior value of variance (s2.post) is Inf
limma
ebayes
updated 5.3 years ago by
Gordon Smyth
45k • written 5.3 years ago by
cemcdono
• 0
1
vote
1
reply
643
views
Limma ebayes function error without any messages
limma
ebayes
updated 6.5 years ago by
Aaron Lun
★ 27k • written 6.5 years ago by
bharata1803
▴ 40
3
votes
3
replies
1.2k
views
Sub : Limma ebayes
limma
ebayes
statistical inference
updated 6.8 years ago by
Gordon Smyth
45k • written 6.8 years ago by
ssrajan86
• 0
0
votes
1
reply
935
views
LmFit and eBayes on merged ESET giving errors
limma
eset
error
ebayes
updated 6.9 years ago by
James W. MacDonald
59k • written 6.9 years ago by
Vani
▴ 20
6
votes
5
replies
1.2k
views
Limma ebayes returns a list with Affy pd.hugene.2.0.st arrays
ebayes
expression
affymetrix
pd.hugene.2.0.st
limma
updated 7.3 years ago by
Gordon Smyth
45k • written 7.3 years ago by
Paulo Nuin
▴ 200
14 results • Page
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Replies
Answer: Robust Multi-array Average could get negative value or not?
by
James W. MacDonald
59k
After running RMA, your data have been logged, base 2. Any value < 1 will have a negative value. Looking at the data from that GEO submissi…
Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
by
Yang Shi
• 0
Got that sir, thanks so much!
Comment: UniprotKB AC/ID to Entrez ID Conversion
by
Guido Hooiveld
★ 3.2k
No, no need to modify `up`. It somehow has to do with the R.BioC version; it works when using the latest versions (R-4.2.0/BioC-3.15), but…
Comment: UniprotKB AC/ID to Entrez ID Conversion
by
tom.kloter
• 0
Thanks a lot for your response! I tried the code in my script and got to the following result: ``` > up <- UniProt.ws(taxId=9606) > up "U…
Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
by
Guido Hooiveld
★ 3.2k
Regarding the normalization method (SCAN); I have only used RMA for the reasons James explained in one of your other threads (https://suppo…
Votes
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
Answer: Print EnhancedVolcano Plot as jpeg or similar in R Notebook
Comment: Print EnhancedVolcano Plot as jpeg or similar in R Notebook
A: coefficient not estimable (limma warning)
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