User: chipolino

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chipolino0
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Posts by chipolino

<prev • 13 results • page 1 of 2 • next >
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Comment: C: DESeq2 gives weird results
... Thank you for your response! Here are the normalized counts: ``` | drug1_1 | drug1_2 | control1 | control2 | |----------|--------------|------- |------ | | 1293.573 | 1144.279 | 90.263 | 118.803 | ``` I also checked the quant.sf files from Salmon for this gene and that's wha ...
written 7 weeks ago by chipolino0
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DESeq2 gives weird results
... Hi, I am doing DE analysis. I have 4 conditions: control, drug1, drug2, drug3 (2 replicates for each condition). I started with Salmon to count transcripts and imported them with tximport. After this I constructed DESeq data set using DESeqDataSetFromTximport following this [tutorial](https://bioco ...
deseq2 salmon written 7 weeks ago by chipolino0 • updated 7 weeks ago by Michael Love24k
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scATAC-seq analysis, data preprocessing
... Hi, During scATAC-seq data preprocessing, does it make sense to filter data matrix, so it contains only most variable peaks (in the same way how we do it for scRNA-seq), before any further dimensionality reduction or clustering analysis? Thanks ...
scatac-seq written 10 weeks ago by chipolino0 • updated 9 weeks ago by Aaron Lun24k
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Comment: C: MDS plot; Batch effects
... But how do I know, if it worked? is there any way to visualize the data again after voom or lmFit/eBayes? ...
written 12 weeks ago by chipolino0
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Comment: C: MDS plot; Batch effects
... Thank you so much for your answer! I have 16 different cell conditions, and 3 replicates for each. 3 replicates are performed in different cell donors (3 donors; 1 replicate for each condition in each donor). My goal is to compare conditions between each other using DGE. Here how the MDS plot looks ...
written 12 weeks ago by chipolino0
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MDS plot; Batch effects
... Hi, I am doing RNA-seq analysis using limma and edgeR, I have 48 samples and 2 batches. I built MDS plots (see below), and now my question is do I have a batch effect I need to correct for or not? My understanding is if batches cluster together on MDS/PCA plot, it's an evidence that batch effects a ...
limma edger rna-seq batches written 12 weeks ago by chipolino0 • updated 12 weeks ago by Aaron Lun24k
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problem with DeMAND, gene expression matrix input
... Hi, I am using DeMAND in my research, the method asks for expression matrix, but I am confused, what expression units it asks for, raw counts? or normalized values like (RPKM, FPKM or TPM)? or it doesn't matter? Also, how bad is it if I have only 3 samples in treatment and control group for overall ...
gene expression demand written 8 months ago by chipolino0
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DEXseq with technical replicates
... Hi everyone, I want to do differential exon usage analysis with DEXseq. I have 3 affected (2 technical replicates for each individual, so 6 samples total) and 3 unaffected individuals  (also 2 technical reps for each sample, 6 samples overall). My question is how should I take into account technica ...
dexseq written 12 months ago by chipolino0 • updated 12 months ago by Alejandro Reyes1.7k
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Comment: C: What doest this p.value distribution mean?
... Thank you, I will check it ...
written 13 months ago by chipolino0
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Comment: C: What doest this p.value distribution mean?
... PCA plot is not great either... Zeros are unaffected patients, Ones are affected. PC2 divides them by gender. ...
written 13 months ago by chipolino0

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