## User: sckinta

sckinta0
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#### Posts by sckinta

<prev • 4 results • page 1 of 1 • next >
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... Hi Aaron, Thanks for your very helpful response! Yes, I do assume that batch effect is the same for every group. Based on the sample preparation information I got, the libraries for the whole experiment were collected and made at three different time/batches, which correspond to the replicate numbe ...
written 5 months ago by sckinta0
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... I have a RNAseq experiment with 5 time points and 2 cell type (2*5=10 conditions) and 3 replicates each. The experiment can be further divided to two sub-experiment -- cell type generation (3 time points * 2 cell types) and cell type re-stimulation (2 time points * 2 cell types) -- since we are not ...
written 5 months ago by sckinta0 • updated 5 months ago by Aaron Lun24k
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... Hi Aaron, I have similar problem as main post. Instead of genotype and treatment, I have cell type and time point, both of which are part of experimental design. The replicate prep batch are the batch here. **Just for visualization purpose**, I used normalizeVSN() result as input for `removeBat ...
written 5 months ago by sckinta0
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... Hi  i have a set of RNAseq data with unbalanced batch effect (see table below). Batch 1 was made of single indexed kit and sequenced at time 1, while batch 2 was made of dual indexed kit and sequenced independently from batch 1.   sample batch groups 1 Naive_Dmt3aKO_r ...
written 11 months ago by sckinta0 • updated 11 months ago by James W. MacDonald50k

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