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Dario Strbenac
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736
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Gerhard Thallinger
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672
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9 months ago • updated 8 months ago
Gerhard Thallinger
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592
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90
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16
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Recent ...
Replies
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
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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?
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Michael Love
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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…
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ATpoint
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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
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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
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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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