User: sckinta

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sckinta480
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Posts by sckinta

<prev • 55 results • page 1 of 6 • next >
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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_rep1 2 Naive_Dmt3aKO ...
R rna-seq edger batch effect written 10 weeks ago by sckinta480 • updated 10 weeks ago by Devon Ryan86k
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Comment: C: Batch effects : ComBat or removebatcheffects (limma package) ?
... Thank you for the tips. I have one more detail question though. According to the clustering and heatmap before batch removal, I have notice batch 1 and 3 are clustered within each group, while all batch 2 samples are clustered together regardless group. In reality, all batch are prepared independent ...
written 3 months ago by sckinta480
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Comment: C: Batch effects : ComBat or removebatcheffects (limma package) ?
... Thank your for sharing this. I am trying to explain your idea in R code using edgeR package. Could you check whether it is right? group <- factor(c("mut","mut","mut","wt","wt","wt")) group <- relevel(group,ref="wt") seq_batch <- factor(c(1,2,3,1,2,3)) design <- model.m ...
written 3 months ago by sckinta480
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Comment: C: RNA-seq replicates not clustering
... Well, only three samples, I cannot say correlation. I do observe outliers have relatively more read count. Here are read count per sample Th2KO_ev_rep1 7,616,704 Th2KO_ev_rep2 3,455,495 Th2KO_ev_rep3 2,867,725 Th2KO_mut_rep1 9,538,351 Th2KO_mut_rep2 5,271,933 Th2KO_mut_rep3 ...
written 3 months ago by sckinta480
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Comment: C: RNA-seq replicates not clustering
... It is just a name. I called vsn as vsnCPM. The plots were made from vsn output. VSN is variance stabilizing method, which is what rlog was trying to do. but rlog is less sensitive to sample size ...
written 3 months ago by sckinta480
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Comment: C: RNA-seq replicates not clustering
... I did remove low exp genes before normalization. Actually I tried to PCA top 50% genes, the results are very similar. I have very low depth on samples. After mapping and filtering, I have only 2M ~ 9M (3M on average) reads left per sample. When I was doing the low exp genes, I just made sure top 3 s ...
written 3 months ago by sckinta480
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Comment: C: RNA-seq replicates not clustering
... This is not CPM. It is vsn output. It is like rlog in DESeq2 ...
written 3 months ago by sckinta480
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Comment: C: RNA-seq replicates not clustering
... So you would just go head with DE analysis with all three replicates? ...
written 3 months ago by sckinta480
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Comment: C: RNA-seq replicates not clustering
... PC1-5 scatterplots: https://ibb.co/nB1Bvp PC1-3 bi-plots: https://ibb.co/iLKaMU ...
written 3 months ago by sckinta480
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RNA-seq replicates not clustering
... I know someone posted similar topics before (https://www.biostars.org/p/315214/ ). However, here, I want to prompt some discussions on this topic with given plots and examples here. I have triplicates for three conditions (Ev. Mut and WT) in mouse cells. I followed standard ways people usually use ...
rna-seq clustering written 3 months ago by sckinta480 • updated 5 weeks ago by Biostar ♦♦ 20

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