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pre-filtering
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6
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4
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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 9.1 years ago by
Michael Love
41k • written 9.1 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
1 of 1
Recent ...
Replies
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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