User: chipolino

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chipolino0
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Posts by chipolino

<prev • 14 results • page 1 of 2 • next >
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How to perform RNA-seq with such MDS plot?
... Hi, I have the following experiment: two cell types (Treg/CD4), 3 donors (52/64/55), 2 batches (24/26), 3 conditions (ha/ut/cd19). My main two questions are the following: 1) what genes are DE in the two cell types (for each condition separately, so Treg/ha vs CD4/ha and so on); 2) What genes are D ...
limma rna-seq batch effect written 6 weeks ago by chipolino0 • updated 6 weeks ago by swbarnes2330
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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 4 months 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 4 months ago by chipolino0 • updated 4 months ago by Michael Love25k
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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 5 months ago by chipolino0 • updated 5 months ago by Aaron Lun25k
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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 5 months 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 5 months 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 5 months ago by chipolino0 • updated 5 months ago by Aaron Lun25k
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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 10 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 15 months ago by chipolino0 • updated 15 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 16 months ago by chipolino0

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