Bioconductor GenomeStudio

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minfi genomestudio methylation

updated 6.1 years ago by James W. MacDonald 63k • written 6.1 years ago by brhead ▴ 40

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GWASTools qualitycontrol HumanOmni5-4BeadChip GenomeStudio illumina

updated 7.1 years ago by Stephanie M. Gogarten ▴ 840 • written 7.1 years ago by Lna • 0

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Comment: DeSEQ 2 Error: some values in assay are negative by James W. MacDonald 63k

In order to back up your assertion that there are no negative values, you should provide evidence. For example ``` any(countData < 0) dds …

Answer: DeSEQ 2 Error: some values in assay are negative by Michael Love 40k

You don't need to remove 0's. What do you get with ``` any(countData < 0) ``` (fixed, typo first time around)

Comment: Interpret plot from DiffBind by Rory Stark ★ 4.9k

See above, you want the sites where `Fold > 0`.

Comment: Interpret plot from DiffBind by Rory Stark ★ 4.9k

That does seem like you have a very high number of open chromatin sites changing. How many are in the consensus matrix? You can see how ma…

Comment: Interpret plot from DiffBind by Rory Stark ★ 4.9k

I can see the confusion here as one color is being used in two different ways. The dark blue/purple color is used for the bars on the left…

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Answer: Interpret plot from DiffBind

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Popular Question to rodrigo.duarte88 ▴ 30

Scholar to Rory Stark ★ 4.9k