Showing : toptable • reset
14
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16
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2.7k
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TopTable Problem : Unique Adj.P.Val which is near 1
limma toptable
7.9 years ago giroudpaul ▴ 40
10
votes
11
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7.6k
views
Standard error and effect size from Limma
effect size Limma toptable Standard Error
updated 8.8 years ago by 50k • written 8.8 years ago by ▴ 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 50k • written 8.1 years ago by ▴ 80
6
votes
7
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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 ★ 28k • written 9.6 years ago by ▴ 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
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 50k • written 15.4 years ago by ▴ 190
0
votes
5
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1.2k
views
eBayes options and decideTests method
limma eBayes decideTests topTable
updated 4.2 years ago by 50k • written 4.2 years ago by • 0
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 ★ 28k • written 8.8 years ago by ▴ 20
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
2
votes
4
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3.7k
views
report genes in intersection of Venn diagram with topTable?
rnaseq venn diagram limma toptable edgeR
updated 8.8 years ago by 50k • written 8.9 years ago by • 0
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 • 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 50k • written 7.6 years ago by ▴ 80
0
votes
3
replies
1.4k
views
Subsetting a data frame generated by topTable() {limma}
limma toptable microarray
updated 4.6 years ago by 50k • written 4.6 years ago by ▴ 30
0
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2
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673
views
Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 12 months ago by 50k • written 12 months ago by • 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 ★ 28k • written 8.2 years ago by ▴ 830
1
vote
2
replies
1.3k
views
differentially expressed genes without contrasts
limma toptable makecontrasts contrast matrix
updated 6.8 years ago by ★ 7.9k • written 6.8 years ago by • 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
2
replies
729
views
decideTests vs topTable results
decideTests topTable limma
updated 10 months ago by 50k • written 10 months ago by ▴ 20
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 ★ 28k • written 6.7 years ago by ▴ 10
0
votes
1
reply
356
views
NAs in some genes in topTable output
limma topTable
updated 15 months ago by 50k • written 15 months ago by ▴ 10
20 results • Page 1 of 1
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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
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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
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