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Answer: problem reading bam files into nucleR
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The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
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It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
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I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
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Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
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Ahmed Salah
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Thank you very much! will take that into consideration
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