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universalmotif, question about enrich_motifs function and number of hits returned
universalmotif
scanning
enrich_motifs
PWM
2.3 years ago
alexandre.blais
▴ 50
2
votes
0
replies
1.6k
views
motifDb PFM vs JASPAR database PFM: conversion to PWM
pwm
pfm
jaspar
motifdb
updated 5.3 years ago by
Bioconductor Community
0 • written 5.4 years ago by
chrisclarkson100
▴ 50
0
votes
0
replies
793
views
Plotting motif enrichment vs background - Jaspar core vertebrates
pwm
motifs
jaspar
meme
motif analysis
5.4 years ago
rbronste
▴ 60
2
votes
1
reply
2.3k
views
Error: unable to find an inherited method for function searchSeq for signature matrix
pwm
tfbstools
jaspar
updated 6.6 years ago by
Ge Tan
▴ 20 • written 6.6 years ago by
chrisclarkson100
▴ 50
0
votes
1
reply
1.2k
views
PWM with columns that add up to 1
biostrings
seqlogo
pwm
updated 7.5 years ago by
Marcel Ramos
690 • written 7.5 years ago by
clausdkuhn
• 0
0
votes
0
replies
850
views
maxScore calculation for 'log2probratio' and 'prob' type PWMs
biostrings
pwm
7.7 years ago
Stefanie Tauber
▴ 40
0
votes
3
replies
1.4k
views
motif scanning using position frequncy matrix of motif in a given set of DNAstringset sequnces?.
motifdb
matchpwm
motif
pwmenrich
pwm
8.5 years ago
vinod.acear
▴ 50
7 results • Page
1 of 1
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Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
Gordon Smyth
50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
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