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25
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7
replies
11k
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Effect of lfcThreshold on p-value in DESeq2
deseq2 rnaseq statistics
updated 6 months ago by ▴ 10 • written 6.5 years ago by ▴ 30
19
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4
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8.1k
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Confidence intervals on edgeR logFC
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updated 8.1 years ago by • 0 • written 9.6 years ago by ▴ 40
10
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14
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13k
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how DESeq calculates p-value ?
deseq differential gene expression statistics p-value
updated 3.1 years ago by ▴ 20 • written 8.2 years ago by ▴ 30
8
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3
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3.2k
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Differing topTable() results with Limma with and without specifying coefficient
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updated 8.0 years ago by 50k • written 8.0 years ago by • 0
8
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8
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6.7k
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Voom transformation from counts and normalization to negative values
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updated 5.6 years ago by ★ 7.9k • written 5.6 years ago by ▴ 60
3
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5
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1.4k
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P adjusted values in Deseq2
DESeq2 Statistics
written 3.3 years ago by • 0
3
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0
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2.2k
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Job: Postdoctoral Scientist, Statistical Bioinformatics and Proteomics, WEHI Australia
job proteomics Job statistics
4.5 years ago • updated 4.3 years ago Gordon Smyth 50k
3
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3
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1.4k
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Using alternative LFC shrinkage methods for computing p-values in DESeq2
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updated 4.9 years ago by 41k • written 4.9 years ago by • 0
2
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2
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2.8k
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How adjusted p-values are calculated in limma
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updated 4.6 years ago by 50k • written 4.6 years ago by ▴ 10
2
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1
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981
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limma for gene expression analysis with big and unbalanced sample size
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updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
2
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3
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1.5k
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RNAseq outlier is a critical sample
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updated 7.9 years ago by 50k • written 7.9 years ago by • 0
2
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2
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7.7k
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edgeR: How is FDR calculated for logFC? (False Discovery Rate)
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7.4 years ago jol.espinoz ▴ 40
2
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4
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1.2k
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Removing batch effect on edgeR when interactons are looked at
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updated 6.6 years ago by ★ 13k • written 6.6 years ago by ▴ 90
2
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845
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21 months ago Andy Lynch ▴ 120
1
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1
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2
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the statistical test that DESeq2 use
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updated 7.2 years ago by ★ 7.9k • written 7.2 years ago by • 0
1
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1
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1.3k
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FPKM t-test vs DEseq2
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updated 12 months ago by ★ 4.0k • written 12 months ago by • 0
1
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6.0 years ago Fred Hutch (Recruiting) ▴ 40
1
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4
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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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5.7 years ago Andrea Carenzo • 0
1
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2
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954
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What to do with microarray probes that catch multiple genes?
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updated 5.7 years ago by 65k • written 5.7 years ago by • 0
1
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2
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930
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Newbie to all of this
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5.5 years ago sportwoo • 0
1
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6
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2.7k
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DESeq2 unbalanced sample size
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updated 14 months ago by 41k • written 5.3 years ago by • 0
1
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0
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9.0 years ago Federico Marini ▴ 150
1
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2
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how to perform pre ranked GSEA in R?
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updated 7.1 years ago by • 0 • written 9.1 years ago by ▴ 80
1
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3.9 years ago Fred Hutch (Recruiting) ▴ 40
1
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Re-calculation of Padj (P adjusted value)
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updated 3.6 years ago by 41k • written 3.6 years ago by ▴ 60
1
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0
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1.8k
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News: Workshop Statistical Methods for Post Genomic Data in Munich, February 12-13, 2015
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9.6 years ago gagneur ▴ 10
1
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1
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341
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Further analysis after limma regression output
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updated 7 months ago by 65k • written 7 months ago by ▴ 10
1
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0
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623
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Statistical test for genomic annotation by ChIPseeker
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20 months ago arisarkar88 ▴ 40
1
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21 months ago Andy Lynch ▴ 120
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2
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comparing two GOstats result lists
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updated 5.9 years ago by 65k • written 5.9 years ago by ▴ 20
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5.8 years ago • updated 3.4 years ago Luo Weijun ★ 1.6k
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Reading large file (15GB) in R
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updated 2.2 years ago by 21k • written 2.3 years ago by ▴ 10
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2.5 years ago • updated 15 months ago Wolfgang Huber ★ 13k
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3
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922
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batch effect in EPIC array data
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updated 14 months ago by ▴ 730 • written 14 months ago by ▴ 10
0
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0
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756
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package for mismatch distribution?
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5.3 years ago myriam.croze07 • 0
0
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1
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964
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Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain empirical p-values?
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5.2 years ago naglemi ▴ 10
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1.3k
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Proteomics data analysis with DEP no replicates
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8 weeks ago Andy Lynch ▴ 120
0
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1
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755
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Exclude interaction terms from the design
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updated 4.5 years ago by 41k • written 4.5 years ago by • 0
0
votes
0
replies
2.0k
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1
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770
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How to handle batch effect and interaction with experimental variables
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4.4 years ago A • 0
0
votes
4
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2.8k
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XCMS for targeted metabolomic/lipidomics/proteomics
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8.3 years ago Titan • 0
0
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3.7 years ago • updated 3.5 years ago whduke • 0
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DEseq2 : Complex design with a mixture of male and female mice
statistics DESeq2
updated 4 months ago by 41k • written 5 months ago by • 0
50 results • Page 1 of 1
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Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
How am i making the data? I am using the DESeq2 output data which I had generated
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k
What do you mean by 'the information'? Do you have things in particular that you want?
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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