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DESeq not working without replicates #46

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mgsrod opened this issue Dec 6, 2022 · 0 comments
Open

DESeq not working without replicates #46

mgsrod opened this issue Dec 6, 2022 · 0 comments

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@mgsrod
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mgsrod commented Dec 6, 2022

Hi,

I'm planning on using Reademption2 to analyse ~10 RNASeq libraries against hundreds on reference sets. I'm testing the system and getting preliminary data using just two libraries and one reference set. Unfortunately I receive the following message when attempting to run the deseq function: "The design matrix has the same number of samples and coefficients to fit,
so estimation of dispersion is not possible. Treating samples as replicates was deprecated in v1.20 and no longer supported since v1.22". I'm not planning on introducing replicates. My understanding is that current versions of DESeq2 provide arguments that allows analysis without replicates but I'm sure if they work through Reademption2. I've tried rolling back DEseq2 to an older version but receive the same message.

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