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Further analysis after limma regression output
statistics Epigenetics limma
updated 5 days ago by 63k • written 5 days ago by ▴ 10
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FPKM t-test vs DEseq2
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batch effect in EPIC array data
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360
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8 months ago alena.vanboemmel • 0
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Results analysis of differential gene expression using DESeq2 package
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updated 9 months ago by ★ 1.3k • written 9 months ago by • 0
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Statistical test for genomic annotation by ChIPseeker
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13 months ago arisarkar88 ▴ 40
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14 months ago Andy Lynch ▴ 120
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6
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896
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regression analysis for epic array methylation data using limma
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16 months ago Jitendra ▴ 10
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Reading large file (15GB) in R
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updated 19 months ago by 21k • written 20 months ago by ▴ 10
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P adjusted values in Deseq2
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750
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News: Ascona Workshop “Biological systems: from first principles to data-​driven modelling and back” 27. 3. - 1. 4. 2022
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23 months ago • updated 8 months ago Wolfgang Huber 13k
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2.5 years ago • updated 2.4 years ago Luo Weijun ★ 1.6k
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734
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2.6 years ago m.jackson • 0
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2.7 years ago António Miguel de Jesus Domingues ▴ 490
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2.8 years ago Laura • 0
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Job: Biostatistics/Bioinformatics Research Scientist at UNC Charlotte
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2.8 years ago • updated 2.5 years ago Luo Weijun ★ 1.6k
1
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753
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Re-calculation of Padj (P adjusted value)
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updated 3.0 years ago by 40k • written 3.0 years ago by ▴ 50
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3.2 years ago • updated 2.9 years ago whduke • 0
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3.3 years ago Fred Hutch (Recruiting) ▴ 40
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3.9 years ago • updated 3.7 years ago Gordon Smyth 48k
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4.6 years ago • updated 3.8 years ago Luo Weijun ★ 1.6k
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1
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542
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How to handle batch effect and interaction with experimental variables
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3.9 years ago A • 0
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1
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572
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Exclude interaction terms from the design
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updated 3.9 years ago by 40k • written 3.9 years ago by • 0
2
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2
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How adjusted p-values are calculated in limma
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updated 4.0 years ago by 48k • written 4.0 years ago by ▴ 10
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766
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Proteomics data analysis with DEP no replicates
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4.1 years ago tatabox • 0
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3
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Using alternative LFC shrinkage methods for computing p-values in DESeq2
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updated 4.3 years ago by 40k • written 4.3 years ago by • 0
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743
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Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain empirical p-values?
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4.6 years ago naglemi ▴ 10
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578
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package for mismatch distribution?
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4.7 years ago myriam.croze07 • 0
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2.2k
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DESeq2 unbalanced sample size
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updated 7 months ago by 40k • written 4.8 years ago by • 0
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749
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Newbie to all of this
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4.9 years ago sportwoo • 0
8
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8
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Voom transformation from counts and normalization to negative values
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updated 5.0 years ago by 7.8k • written 5.0 years ago by ▴ 50
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757
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What to do with microarray probes that catch multiple genes?
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updated 5.1 years ago by 63k • written 5.1 years ago by • 0
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Do the gene set statistics of the ROAST paper correspond to those implemented in the .roastEffects R function?
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5.1 years ago Andrea Carenzo • 0
0
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2
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870
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comparing two GOstats result lists
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updated 5.3 years ago by 63k • written 5.3 years ago by ▴ 20
1
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0
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929
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Job: Statistical Research Associate
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5.4 years ago Fred Hutch (Recruiting) ▴ 40
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DSS DMLTest Prior Estimate of theta dispersion
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5.5 years ago floriandeckert ▴ 30
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913
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News: SCANGEN: Single-cell cancer genomics workshop at ISMB 2018
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5.5 years ago kieranrcampbell ▴ 50
0
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0
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936
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Two questions about pathifier package
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5.7 years ago arronar • 0
24
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6
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9.0k
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Effect of lfcThreshold on p-value in DESeq2
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updated 6.0 years ago by 63k • written 6.0 years ago by ▴ 30
2
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4
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978
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Removing batch effect on edgeR when interactons are looked at
rnaseq edger statistics model matrix
updated 6.0 years ago by 13k • written 6.0 years ago by ▴ 70
0
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0
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964
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Assigning stats to differential peak locations relative to TSS
chipseeker chipseq statistics
6.0 years ago rbronste ▴ 60
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0
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1.3k
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Job: Research Scientist in Biostatistics/Bioinformatics
statistics genetics genomics R Job
6.6 years ago • updated 6.5 years ago Luo Weijun ★ 1.6k
1
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2
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1.8k
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how to perform pre ranked GSEA in R?
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updated 6.6 years ago by • 0 • written 8.6 years ago by ▴ 80
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0
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1.1k
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Job: Bioinformaticist, Research Programmer
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6.6 years ago radel • 0
1
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2.5k
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the statistical test that DESeq2 use
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updated 6.6 years ago by 7.8k • written 6.6 years ago by • 0
2
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2
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6.8k
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edgeR: How is FDR calculated for logFC? (False Discovery Rate)
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6.8 years ago jol.espinoz ▴ 40
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0
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1.4k
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Job: PhD Positions in Computational Cancer Research
computational biology image analysis cancer genomics statistics Job
6.8 years ago Bernd Fischer ▴ 550
50 results • Page 1 of 1
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Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0
I´m sorry causing confusion here, but the gene matrices I refer to are actually obtained via https://nf-co.re/rnaseq. The problem with the…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
For the reasons outlined in the Soneson paper, I'd prefer this pipeline: https://nf-co.re/rnaseq You cannot use these scaled TPM approach…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0
I get your point as we already starting with TPM. This was more to clarify that I understand the principle correctly. However, further I´m…
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batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
Answer: Batch correction and repeated measures
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