User: sckinta

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sckinta0
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Posts by sckinta

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Comment: C: subset samples for RNAseq differential analysis
... 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 9 weeks ago by sckinta0
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subset samples for RNAseq differential analysis
... 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 ...
limma edger rnasq written 9 weeks ago by sckinta0 • updated 9 weeks ago by Aaron Lun23k
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Comment: C: removeBatchEffect -- warnings and results
... 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 9 weeks ago by sckinta0
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RNA-seq unbalanced batch effect correction
... 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 ...
rnaseq edger batch effect written 8 months ago by sckinta0 • updated 8 months ago by James W. MacDonald50k

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