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Option to specify control genes for fitting size factors #204

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mbernste opened this issue Nov 15, 2023 · 0 comments
Open

Option to specify control genes for fitting size factors #204

mbernste opened this issue Nov 15, 2023 · 0 comments
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enhancement New feature or request

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@mbernste
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mbernste commented Nov 15, 2023 •
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The original DESeq2 package enables one to specify "control genes" that are used to fit the size factors. These are genes that are not expected to be changing between samples. See: https://www.rdocumentation.org/packages/DESeq2/versions/1.12.3/topics/estimateSizeFactors

It would be great if the "deseq2" function and "fit_size_factors" function enabled the user to pass a list of control genes that would be used to estimate the size factors. These genes should be a subset of the genes in the full dataset.
@BorisMuzellec BorisMuzellec added the enhancement New feature or request label Nov 16, 2023
@BorisMuzellec BorisMuzellec added the good first issue Good for newcomers label Mar 4, 2024
@BorisMuzellec BorisMuzellec removed the good first issue Good for newcomers label Mar 29, 2024
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@mbernste @BorisMuzellec