User: kris275

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kris2750
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Posts by kris275

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Comment: C: Design and contrast matrices for including batch effect
... Dear swbarnes2, thank you for your reply. In this case the experiment was done in different **batches**, the batches were included as **"lanes"**. I could have clarified this better with another variable name, but the batch to batch variability is definitely there- visible with dendrograms and mds ...
written 12 days ago by kris2750
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Design and contrast matrices for including batch effect
... Hello everyone, I am working on a RNA-seq project that includes samples from normal tissue, adenomas, adenocarcinomas, liver metastases and was done in five batches. As I have previously read, it is best if batch effect is included in the design matrix for linear model fitting- shown in limma guid ...
R design contrasts rna-seq batch effect written 13 days ago by kris2750 • updated 12 days ago by swbarnes29.4k

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