User: chipolino

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chipolino0
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Posts by chipolino

<prev • 11 results • page 1 of 2 • next >
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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 9 days ago by chipolino0 • updated 8 days ago by Aaron Lun23k
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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 24 days 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 25 days 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 25 days ago by chipolino0 • updated 25 days ago by Aaron Lun23k
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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 6 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 10 months ago by chipolino0 • updated 10 months ago by Alejandro Reyes1.6k
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Comment: C: What doest this p.value distribution mean?
... Thank you, I will check it ...
written 11 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 11 months ago by chipolino0
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What doest this p.value distribution mean?
... Hi everyone, I am doing an RNA-seq analysis with DESeq2. I have 3 patients with disease (affected) and 3 healthy patients (unaffected). After following standard DESeq2 pipeline (as described here), I got my table with results and p.value column. I decided to check the distribution of p.values and h ...
deseq2 pvalue written 11 months ago by chipolino0 • updated 11 months ago by Michael Love23k
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Comment: C: limma RNA-seq analysis of human data
... Thank you for your reply, In RNA-seq how do you usually handle technical replicates? Do you just analyze them independently (like I did here) or should you sum up the raw count from these replicates? According to this question (https://support.bioconductor.org/p/97390/) you should do summation, am ...
written 13 months ago by chipolino0

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