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Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
4 months ago
pl23
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R session aborted: prcomp
Biobase
stats
updated 3.0 years ago by
Kevin Blighe
★ 3.9k • written 3.1 years ago by
Gero
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Job:
Two Post-doctoral Positions at University of Campinas
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7.7 years ago • updated 7.6 years ago
Benilton Carvalho
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Job:
Data Scientist / Bioinformatician / Statistician at University of California
R
python
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bioinformatics
perl
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7.7 years ago
clif.duhn
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6
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getting a matrix with diagonal =1
stats
updated 8.3 years ago by
Aaron Lun
★ 28k • written 8.3 years ago by
Angel
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3
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3
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2.2k
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ribosome profiling analysis with different dispersions
deseq2
linear model
ribosome profiling
stats
updated 8.7 years ago by
Ryan C. Thompson
★ 7.9k • written 8.7 years ago by
Jake
▴ 90
2
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2
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2.2k
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Memory management in R
stats
updated 9.1 years ago by
Martin Morgan
25k • written 9.1 years ago by
mrk.carty
▴ 30
2
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5
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Download the stats of Bioconductor
bioconductor
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9.3 years ago
Lluís Revilla Sancho
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Comment: Which input file is used for DGEList in EgdeR?
by
Michael Love
41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Michael Love
41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts
by
Michael Love
41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
Comment: Estimating Cell Counts for EPIC V2 array data
by
normawiedman059
• 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
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A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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