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Showing :
toptable
•
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14
votes
16
replies
2.7k
views
TopTable Problem : Unique Adj.P.Val which is near 1
limma
toptable
7.9 years ago
giroudpaul
▴ 40
11
votes
5
replies
13k
views
Limma: how to get same output as topTable but for all the genes ?
limma
toptable
updated 6.8 years ago by
Gordon Smyth
50k • written 15.4 years ago by
Daren Tan
▴ 190
10
votes
11
replies
7.6k
views
Standard error and effect size from Limma
effect size
Limma
toptable
Standard Error
updated 8.8 years ago by
Gordon Smyth
50k • written 8.8 years ago by
Vani
▴ 20
8
votes
10
replies
4.8k
views
Interpretation of confidence interval values for logFC returned from topTable function in limma with microarray dataset
limma
topTable
confidence interval
effect size
microarray
updated 8.1 years ago by
Gordon Smyth
50k • written 8.1 years ago by
Konstantinos Yeles
▴ 80
6
votes
4
replies
1.2k
views
Limma outputs different results for same sample?
topTable
MicroarrayData
ebayes
limma
Microarray
3.2 years ago
snijesh
▴ 20
6
votes
7
replies
2.2k
views
what causes the difference in the topTable results by the two analyses using limma?
limma
topTable
updated 9.6 years ago by
Aaron Lun
★ 28k • written 9.6 years ago by
Rao,Xiayu
▴ 550
3
votes
6
replies
2.2k
views
Help to understand my contrast.matrix and to interpret my topTable results
contrast matrix
toptable
makecontrasts
differential gene expression
6.6 years ago
stinehedensted
• 0
3
votes
3
replies
2.1k
views
Explanation of an ANOVA approach of multiple coefficients in limma with topTable in a microarray analysis
limma
ANOVA
topTable
microarray
updated 7.6 years ago by
Gordon Smyth
50k • written 7.6 years ago by
Konstantinos Yeles
▴ 80
2
votes
4
replies
2.8k
views
Meta-Analysis after running limma on a normalized dataset
meta-analysis
limma
toptable
updated 8.8 years ago by
Aaron Lun
★ 28k • written 8.8 years ago by
Vani
▴ 20
2
votes
4
replies
2.3k
views
Why my limma DEG result in top Table all without significant meaning,showing logFC <1.5 or logFC>-1.5 ?
limma
toptable
deg
logfc
written 5.6 years ago by
Biomed
• 0
2
votes
4
replies
3.7k
views
report genes in intersection of Venn diagram with topTable?
rnaseq
venn diagram
limma
toptable
edgeR
updated 8.8 years ago by
Gordon Smyth
50k • written 8.9 years ago by
MBWatson
• 0
2
votes
2
replies
2.0k
views
Error while calling function topTable() from limma R package in microarray data analysis
limma
microarray
a4Core
topTable
statistical inference
updated 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 years ago by
svlachavas
▴ 830
1
vote
2
replies
1.3k
views
differentially expressed genes without contrasts
limma
toptable
makecontrasts
contrast matrix
updated 6.8 years ago by
Ryan C. Thompson
★ 7.9k • written 6.8 years ago by
hoe
• 0
1
vote
1
reply
1.7k
views
limma: The topTable function implementation when outputin the differential expression results from RNA-seq dataset?
limma
voom
edgeR
toptable
output
updated 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
heikki.sarin
▴ 10
0
votes
3
replies
1.4k
views
Subsetting a data frame generated by topTable() {limma}
limma
toptable
microarray
updated 4.6 years ago by
Gordon Smyth
50k • written 4.6 years ago by
Alexander Azarian
▴ 30
0
votes
5
replies
1.2k
views
eBayes options and decideTests method
limma
eBayes
decideTests
topTable
updated 4.2 years ago by
Gordon Smyth
50k • written 4.2 years ago by
irene.roman
• 0
0
votes
2
replies
959
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable
voom
contrasts
2.7 years ago
James
• 0
0
votes
1
reply
356
views
NAs in some genes in topTable output
limma
topTable
updated 15 months ago by
Gordon Smyth
50k • written 15 months ago by
thkapell
▴ 10
0
votes
2
replies
729
views
decideTests vs topTable results
decideTests
topTable
limma
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
Anna
▴ 20
0
votes
2
replies
673
views
Full list of differential genes not obtained in topTable
Microarray
GEOquery
topTable
limma
updated 12 months ago by
Gordon Smyth
50k • written 12 months ago by
Ankita
• 0
20 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
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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