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GOexpress
•
reset
0
votes
2
replies
873
views
Can't install GO.db
GOexpress
GO.db
GOSemSim
10 months ago
Chruut
• 0
2
votes
8
replies
700
views
Errors when plotting data using heatmap_GO (GOexpress)
GOexpress
updated 11 months ago by
kevin.rue
▴ 320 • written 11 months ago by
grolo
• 0
0
votes
0
replies
345
views
GOexpress pvalue and gene sets
GOexpress
19 months ago
jms2520
• 0
0
votes
4
replies
813
views
GOexpress - Error when plotting expression data
RNA-seq
transcriptomics
gene ontology
gene expression
GOexpress
updated 3.7 years ago by
kevin.rue
▴ 320 • written 3.7 years ago by
atorson
• 0
1
vote
2
replies
977
views
Obtain the first gene expression heatmaps from GOexpress package gene ontology enrichment analysis results
GOexpress
heatmap
gene ontology
plot
updated 4.0 years ago by
kevin.rue
▴ 320 • written 4.0 years ago by
Antonio Campos
• 0
0
votes
2
replies
804
views
'GO_analyse' function error
goexpress
ExpressionSet
GO_analyse
4.1 years ago
rezashiralmohammad
• 0
2
votes
4
replies
1.0k
views
GOexpress - Trouble with subset_scores result (<0 rows>)
GOexpress
subset_scores
<0 rows>
5.7 years ago
sina.zboron
• 0
9
votes
8
replies
3.3k
views
heatmap of genes based on enriched GO categories
goexpress
gopro
6.6 years ago
Bogdan
▴ 660
5
votes
4
replies
1.3k
views
Contrasts in GOexpress analysis?
gene ontology
goexpress
updated 6.7 years ago by
kevin.rue
▴ 320 • written 6.7 years ago by
mforde84
▴ 20
0
votes
3
replies
3.3k
views
Gene ontology and pathway analysis in R - replicate ToppGene features; best strategy for getting annotations?
topgo
biomart
gene ontology
goexpress
pathway analysis
updated 7.4 years ago by
kevin.rue
▴ 320 • written 7.4 years ago by
Darya Vanichkina
▴ 120
2
votes
6
replies
2.4k
views
GOexpress: GO_analyse function throws Error: Space required after the Public Identifier
goexpress
updated 7.6 years ago by
kevin.rue
▴ 320 • written 7.6 years ago by
martin.hoelzer
▴ 20
3
votes
2
replies
1.1k
views
Is it common to get all 0 values when running the randomForest step in GOexpress?
goexpress
updated 7.9 years ago by
kevin.rue
▴ 320 • written 7.9 years ago by
willj
▴ 30
3
votes
6
replies
1.5k
views
GOexpress error at pValue_GO step
software error
goexpress
updated 7.9 years ago by
kevin.rue
▴ 320 • written 7.9 years ago by
kcamnairb
▴ 10
6
votes
7
replies
3.3k
views
GOexpress: use DESeq2 data object as input
GOexpress
deseq2
expressionset
8.0 years ago
martin.hoelzer
▴ 20
14 results • Page
1 of 1
Recent ...
Replies
Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
by
Michael Love
40k
Did you manually calculate RPMs? Try `fpm(dds)` for comparison, as this also uses DESeq2 median ratio scaling.
Comment: collapseReplicates error after tximeta
by
Michael Love
40k
A note: I've now changed collapseReplicates() to output a loud warning when it is run on a DESeqDataSet (SummarizedExperiment) with more th…
Comment: Suggested package missing from Development version of Bioconductor
by
shepherl
3.5k
Have you tried reaching out to the maintainers? If they do not fix the package it will remain unavailable and cause ERROR in your package.…
Answer: Batch effect adjust in model matrix
by
ATpoint
★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
by
Michael Love
40k
Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …
Votes
Comment: Batch correction and repeated measures
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
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