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Number of rows in DESeq2 output (.csv) is not the same as number of rows in the results(dds) dataframe
output
difference
22 months ago
Jamie
• 0
0
votes
3
replies
1.7k
views
DECIPHER save alignement in outputs
msa
decipher
output
prettyPrint
updated 3.6 years ago by
UBod
▴ 290 • written 3.6 years ago by
matamunee
• 0
3
votes
6
replies
1.4k
views
Interpreting the output of score test using GENESIS
genesis
output
score
updated 4.6 years ago by
Stephanie M. Gogarten
▴ 870 • written 4.6 years ago by
lassana.a.samarakoon
▴ 10
0
votes
3
replies
1.3k
views
MEDIPS - Annotation output explanation
MEDIPS
Output
6.0 years ago
vjain
• 0
2
votes
8
replies
4.2k
views
How to extract the voom normalized value for each observation?
voomWithQualityWeights
output
updated 6.4 years ago by
Gordon Smyth
50k • written 6.4 years ago by
harelarik
▴ 60
1
vote
1
reply
1.7k
views
limma: The topTable function implementation when outputin the differential expression results from RNA-seq dataset?
limma
voom
edgeR
toptable
output
updated 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
heikki.sarin
▴ 10
2
votes
9
replies
3.2k
views
msa alignement: sorted sequences by sequence name
msa
alignement
output
sorted
7.2 years ago
Olorin
▴ 50
2
votes
2
replies
1.3k
views
Cytofkit - Trouble with writing files after performing the analysis
cytofkit
cytof
write.csv
output
updated 7.5 years ago by
chen_hao
▴ 30 • written 7.5 years ago by
cjackson13
• 0
0
votes
5
replies
6.2k
views
Adding information to the DESeq2 output file (gene name and expression levels for each sample(
deseq2
gene
columns
output
updated 8.5 years ago by
Michael Love
41k • written 8.5 years ago by
amyfm
▴ 10
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
That's an assumption used for normalization of a sample, not an assumption you can use for an individual model. We always normalize to atte…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
SamGG
▴ 350
Is useless the assumption that the majority of genes have no variation in expression (bearing in mind that they are distributed over the en…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list?
by
James W. MacDonald
65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list?
by
bandconductor
• 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Votes
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
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