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pre-filtering
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6
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4
replies
2.6k
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discrepance in DESeq2 results with different design structures
deseq2
differential expression
independent filtering
pre-filtering
design matrix
9.0 years ago
Assa Yeroslaviz
★ 1.5k
5
votes
8
replies
6.7k
views
DESeq2: Applying different pre-filtering for DE and EDA/Visualization of RNASeq data
deseq2
pre-filtering
updated 7.2 years ago by
Michael Love
41k • written 7.2 years ago by
Zach Roe
▴ 10
1
vote
1
reply
1.9k
views
Does manual pre-filtering of the data on read counts violate the assumptions of the dispersion estimation in DESeq2?
deseq2
pre-filtering
updated 9.0 years ago by
Michael Love
41k • written 9.0 years ago by
Johannes Rainer
★ 2.0k
0
votes
2
replies
1.3k
views
Error with DEXSeqDataSet object after performing pre-filter
DEXSeq
rownames
pre-filtering
updated 8.3 years ago by
Wolfgang Huber
★ 13k • written 8.3 years ago by
arom2
• 0
1
vote
6
replies
1.9k
views
Nonspecific filtering of microarray data
microarray
affymetrix microarrays
pre-filtering
filtering
nonspecific filtering
updated 6.9 years ago by
Wolfgang Huber
★ 13k • written 6.9 years ago by
n.lu
• 0
3
votes
7
replies
5.0k
views
Pre-filtering genes counts vs normalised counts DESeq2
deseq2
pre-filtering
updated 6.0 years ago by
Michael Love
41k • written 6.0 years ago by
bekah
▴ 40
6 results • Page
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Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs
by
Guangchuang Yu
★ 1.2k
an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.
Comment: Trying to use enrichGO
by
Guido Hooiveld
★ 3.9k
Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
Comment: Different Shrunk Log2FC according with reference
by
andrebolerbarros
▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
ATpoint
★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Answer: Different Shrunk Log2FC according with reference
by
ATpoint
★ 4.0k
Please see: https://support.bioconductor.org/p/p134551/ I asked basically the same before. In short, reference level might have an influ…
Votes
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
Comment: get BM error
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
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ATpoint
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Gordon Smyth
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i.sudbery
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Michael Love
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shepherl
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