Showing : toptable • reset
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729
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decideTests vs topTable results
decideTests topTable limma
updated 10 months ago by 50k • written 10 months ago by ▴ 20
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2
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673
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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
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1
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356
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NAs in some genes in topTable output
limma topTable
updated 15 months ago by 50k • written 15 months ago by ▴ 10
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2
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959
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limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
2.7 years ago • updated 2.6 years ago James • 0
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4
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2.3k
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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
6
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4
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1.2k
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Limma outputs different results for same sample?
topTable MicroarrayData ebayes limma Microarray
3.2 years ago snijesh ▴ 20
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5
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1.2k
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eBayes options and decideTests method
limma eBayes decideTests topTable
updated 4.2 years ago by 50k • written 4.2 years ago by • 0
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3
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1.4k
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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
3
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6
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2.2k
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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
1
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1
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1.7k
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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
11
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5
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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
1
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2
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1.3k
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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
3
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3
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2.1k
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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
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
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10
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4.8k
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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
2
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2
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2.0k
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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
2
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4
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2.8k
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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
10
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11
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7.6k
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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
2
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4
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3.7k
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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
6
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7
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2.2k
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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
20 results • Page 1 of 1
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Comment: 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…
Comment: get BM error by Fara • 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Answer: get BM error by James W. MacDonald 65k
The genes you present are orthologous mappings from D. rerio to other teleost fishes, so it is probably going to be difficult to map to NCB…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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