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42
votes
2
answers
37k
views
21 follow
2
answers
conceptual question about FDR, FDR adjusted p-value and q-value
qvalue fdr written 7.0 years ago by Jack Luo • 410 • updated 3.2 years ago by Gordon Smyth ♦ 39k
9
votes
2
answers
34k
views
7 follow
2
answers
[DESEQ2] How to access the normalized data of a DESeqDataSet
deseq2 written 4.7 years ago by john • 70 • updated 4.7 years ago by Steve Lianoglou ♦ 12k
1
vote
2
answers
31k
views
2
answers
error in hclust function
written 7.5 years ago by Alyaa Mahmoud • 440 • updated 7.5 years ago by Thomas Girke • 1.7k
0
votes
4
answers
30k
views
4
answers
how to set R memory limit
written 7.9 years ago by wang peter • 2.0k • updated 7.9 years ago by Sunny Yu Liu • 80
8
votes
1
answer
28k
views
8 follow
1
answer
DESeq2 output explanation
deseq deseq2 written 5.1 years ago by francesca.defilippis • 60 • updated 5.1 years ago by Michael Love ♦ 26k
0
votes
1
answer
26k
views
1
answer
no method for coercing S4 class to a vector
written 5.3 years ago by Guest User • 12k • updated 5.2 years ago by Andrzej Oleś • 720
14
votes
2
answers
24k
views
10 follow
2
answers
heatmap.2() get matrix after hierarchical clustering
clustering written 7.2 years ago by Guest User • 12k • updated 7.2 years ago by Thomas Girke • 1.7k
0
votes
0
answers
23k
views
0
answers
Why the resuts are so different between the classic and the glm methods?
edger written 6.0 years ago by Jiantao Yu • 10
2
votes
1
answer
21k
views
1
answer
Row labels in a heatmap
microarray written 7.4 years ago by Liat Shavit Grievink • 60 • updated 7.4 years ago by James W. MacDonald ♦ 52k
0
votes
1
answer
21k
views
1
answer
Error in plot.window(...) : need finite 'xlim' values
written 11.1 years ago by T Joshi • 90 • updated 11.1 years ago by Sean Davis ♦ 21k
2
votes
1
answer
20k
views
1
answer
Installing Bioclite.R Package
install bioclite written 4.0 years ago by louiseapps2 • 0
0
votes
1
answer
20k
views
1
answer
Upgrading Bioconductor using BiocUpgrade
biocinstaller written 7.1 years ago by Lavinia Gordon • 480 • updated 7.1 years ago by Dan Tenenbaum • 8.2k
13
votes
1
answer
20k
views
1
answer
RPKM, CPM and TMM
rnaseq edger differential expression written 4.4 years ago by Pauly Lin • 110 • updated 4.4 years ago by Aaron Lun • 25k
5
votes
3
answers
19k
views
3
answers
BLAST in R
written 8.5 years ago by Zoha Moztarzadeh • 20 • updated 4.0 years ago by mhahsler • 20
15
votes
0
answers
18k
views
11 follow
0
answers
limma moderated t-statistics and B-statistics
microarray limma written 15.2 years ago by Gordon Smyth ♦ 39k
29
votes
3
answers
17k
views
14 follow
3
answers
Batch correction in DESeq2
rnaseq deseq2 combat removebatcheffect() batch effect written 4.0 years ago by AB • 70 • updated 3.5 years ago by adam • 0
16
votes
2
answers
17k
views
9 follow
2
answers
deseq2 filter the low counts
deseq2 lowcount written 4.8 years ago by aristotele_m • 30 • updated 3.2 years ago by pkachroo • 10
8
votes
1
answer
17k
views
1
answer
DESeq2 baseMean counts
deseq2 written 4.0 years ago by zpingfeng • 0 • updated 4.0 years ago by Michael Love ♦ 26k
10
votes
2
answers
16k
views
2
answers
FDR and padj in deseq and edger
edger deseq2 written 4.1 years ago by tonja.r • 40 • updated 4.1 years ago by Gordon Smyth ♦ 39k
0
votes
4
answers
15k
views
4
answers
installation packages
written 6.2 years ago by fran vino • 40 • updated 6.2 years ago by Steve Lianoglou ♦ 12k
0
votes
1
answer
14k
views
1
answer
Unable to find an inherited method for function ‘exprs’
biobase geoquery virtualarray written 6.3 years ago by Dave Tang • 210 • updated 6.3 years ago by Wolfgang Huber ♦ 13k
1
vote
1
answer
14k
views
1
answer
reading fasta file into R
biostrings written 7.4 years ago by Guest User • 12k • updated 7.4 years ago by Vincent J. Carey, Jr. ♦ 6.3k
12
votes
2
answers
14k
views
11 follow
2
answers
Differential expression of FPKM from RNA-seq data using limma and voom()
limma written 6.0 years ago by Jon Bråte • 160 • updated 3.4 years ago by Gordon Smyth ♦ 39k
8
votes
3
answers
14k
views
6 follow
3
answers
Design formula and Design matrix in DESeq
rnaseq limma deseq2 formula written 4.6 years ago by AurelieMLB • 50
3
votes
0
answers
14k
views
0
answers
"Error in readRDS(file) : unknown input format" appearing every time starting Rstudio after BiocUpgrade
bioconductor biocupgrade rstudio r3.2.2 written 4.1 years ago by svlachavas • 740
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