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deseq2 multifactor interaction term gender effect 3-factors

updated 5.0 years ago by Michael Love 41k • written 5.0 years ago by kmu004 ▴ 50

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756

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deseq2 interaction term

5.6 years ago guipagui • 0

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deseq2 interaction term

updated 5.6 years ago by Michael Love 41k • written 5.6 years ago by Cece • 0

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deseq2 extracting contrasts rnaseq interaction term

updated 5.8 years ago by swbarnes2 ★ 1.3k • written 5.8 years ago by Amit Indap ▴ 10

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deseq2 lfcshrink interaction term

updated 6.0 years ago by Michael Love 41k • written 6.0 years ago by krutherford • 0

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deseq2 interaction term multiple groups betaprior

updated 6.0 years ago by Michael Love 41k • written 6.0 years ago by tarun2 • 0

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deseq2 multiple factor design interaction term

updated 6.1 years ago by Michael Love 41k • written 6.1 years ago by Giovanni Bacci • 0

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deseq2 design interaction term R

6.2 years ago • updated 6.1 years ago briverog • 0

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deseq2 ANOVA design interaction term

updated 6.2 years ago by Michael Love 41k • written 6.2 years ago by tarun2 • 0

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deseq2 sva interaction term grouping variable deseq

6.2 years ago kevin.kingsland ▴ 70

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deseq2 interaction term

updated 6.6 years ago by Michael Love 41k • written 6.6 years ago by sofiagreen72211 ▴ 10

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deseq2 multiple factor design nested design interaction term

updated 6.9 years ago by Michael Love 41k • written 7.0 years ago by zahra.aboukhalil • 0

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deseq2 deseq limma interaction term

updated 7.0 years ago by Simon Anders ★ 3.7k • written 7.0 years ago by sbcn ▴ 80

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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…

Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10

Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…

Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k

I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…

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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

Comment: biomaRt : No lock file for BiocFileCache

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