User: harry.smith

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harry.smith20
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Posts by harry.smith

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Comment: C: Visualise and remove batch effects in DESeq2
... You might consider looking into RUV ('RUVSeq' in bioconductor)  with 1 nuisance variable since you are trying to address one batch effect. I have had some success with this, but be careful as the RUV method can sometimes over normalize your data and remove the biological variance you are interested ...
written 10 months ago by harry.smith20
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Should I use alpine and can I convert the output back to counts?
... Hello, I am working with some paired-end data, and based on the fastQC reports the R2 reads have pretty bad GC, frag length, and base-pair results. I am worried that using these R2s will add bias related to the issues above. First, I tried just using the R1s with RSEM, but got extremely poor alignm ...
deseq2 alpine written 12 months ago by harry.smith20 • updated 12 months ago by Michael Love24k

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