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EdgeR: setting reference condition and design matrix headers
edgeR
reference
design matrix
multiple factor design
updated 8.9 years ago by
Aaron Lun
★ 28k • written 8.9 years ago by
Ekarl2
▴ 80
3
votes
3
replies
1.8k
views
EnsDb.Rnorvegicus for Rnor6
annotation
db
reference
rnor6
updated 3.8 years ago by
Guido Hooiveld
★ 3.9k • written 3.8 years ago by
keremwai
• 0
0
votes
2
replies
1.1k
views
sigh of log2FC values in DESeq2
sign
FoldChange
DESeq2
reference
updated 2.3 years ago by
Michael Love
41k • written 2.3 years ago by
yampolsk
• 0
2
votes
2
replies
1.1k
views
Tximport missing values for group summarizing counts
tximport
rat
reference
GTF
salmon
3.8 years ago
keremwai
• 0
0
votes
2
replies
1.0k
views
Reference manual for rmr2 package
reference
updated 8.5 years ago by
Aaron Lun
★ 28k • written 8.5 years ago by
Agaz Hussain Wani
▴ 260
0
votes
0
replies
818
views
Setting relevel with the JunctionSeq package
junctionseq
relevel
reference
7.2 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
0
replies
803
views
Reference for minimum number of probes commonly used for segmentation of microarray data
segmentation
reference
CNA
TCGA
5.2 years ago
jlarsen728
• 0
7 results • Page
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Answer: Error retrieving ensembl gene id using biomaRt...
by
Mike Smith
★ 6.5k
I think you have the assignment operator (`<-`) the wrong way round. It should be `df_biomrt_tmp <- getBM(...`
Answer: Error retrieving ensembl gene id using biomaRt...
by
James W. MacDonald
65k
I can't reproduce. ``` > library(biomaRt) Warning message: package 'biomaRt' was built under R version 4.3.2 > library(org.Hs.eg.db…
Comment: DESeq2 setting significant p-value
by
Michael Love
41k
``` > counts <- matrix(1:16, ncol=4, dimnames=list(letters[1:4],NULL)) > coldata <- data.frame(x=1:4) > DESeqDataSetFromMatrix(counts, cold…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
Right, I was suggesting subsetting as a valid choice for "treatment and control samples at each timepoint"
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Fair enough, I guess it depends on the comparison being made, right? If one was interested in a feature comparing Timepoint A vs B, then it…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
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
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