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Posts by harry.smith
... 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 ...
... 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 ...
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