User: tlorin

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tlorin210
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Switzerland
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14 hours ago
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2 years, 8 months ago
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Posts by tlorin

<prev • 52 results • page 1 of 6 • next >
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Comment: C: Minimal TPM threshold for qPCR measure of gene expression
... Then, which TPM would be a "piece of cake"? ;-) In other words, if you had to advise someone doing qPCR in your lab, would you consider a TPM of 2/5/10 as relevant for first test? (Keeping in mind that this will be highly dependent on the factors you mentioned above) ...
written 12 days ago by tlorin210
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Comment: C: Minimal TPM threshold for qPCR measure of gene expression
... @ATPoint do you mean that the detection would greatly vary from one gene to another and from one experiment to another? (Sorry, I'm not familiar with molecular biology yet...). Hence, I presume the TPM would not "mean" much and a gene with a TPM of 0.1 could be detected by qPCR while a gene with a T ...
written 12 days ago by tlorin210
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Comment: C: Minimal TPM threshold for qPCR measure of gene expression
... To be sure that I correctly understand, with a TPM threshold of **1** I would (roughly) be able to detect candidate gene expression with ~50 ng total RNA? ...
written 12 days ago by tlorin210
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Minimal TPM threshold for qPCR measure of gene expression
... Hello, I am not a molecular biologist and I am mostly doing RNA-Seq. I want to find marker genes based on RNA-Seq results and I have to discuss with people at the bench about candidate genes would be good markers. These genes should thus have a measurable expression using qPCR. I am wondering what ...
tximport tpm qpcr rna-seq kallisto written 12 days ago by tlorin210
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Comment: C: Principal Component Analysis: How many most variable genes should I take?
... > I think that it still depends on what is being segregated by your PC1: if it is clearly segregating one time-point from another This is indeed the case: with `ntop=500` PC1 segregates the time points quite well. If I increase `ntop`, this "time" signal is no longer visible on the sole PC1 and ...
written 28 days ago by tlorin210
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Comment: C: Principal Component Analysis: How many most variant genes should I take?
... @Kevin Blighe Thanks for your answer! My data is a timeseries dataset with 21 sample points, so not disease vs control (I don't know if that would change your point?). I added this precision in the post above. ...
written 29 days ago by tlorin210
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Principal Component Analysis: How many most variable genes should I take?
... I want to plot my data (timeseries dataset) using PCA and am wondering how many "most variable" genes I should take. For instance, in DESeq2, the default for `plotPCA` is `ntop=500`, but why not 1,000 or simply all genes? I saw on [this page][1] that > It's a tradeoff between computational eff ...
deseq2 rna-seq written 4 weeks ago by tlorin210 • updated 28 days ago by MAPK1.1k
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Comment: C: Difference between heatmap using Euclidian distance and Poisson distance
... I understand much better now, thanks. >If you apply both to the correct data, then you should generally see the same or very similar result. That's indeed the case. ...
written 4 weeks ago by tlorin210
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Difference between heatmap using Euclidian distance and Poisson distance
... *(This thread is related to a Bioconductor package so I also posted this question on the [dedicated forum][1]. However, I thought this could relate to bioinformatics in general.)* Using DESeq2 I would like to obtain a heatmap of sample-to-sample distances using the rlog-transformed values. However, ...
deseq2 poisson rna-seq heatmap written 4 weeks ago by tlorin210 • updated 4 weeks ago by Kevin Blighe6.7k
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Comment: C: Convert Gene Name to RefSeq ID
... @genomax: how would you do with a complete gene name instead of the shortcut? For instance `Stegastes partitus phosphoribosyl transferase domain containing 1`. This command does not output anything: ```./esearch -db nuccore -query "Stegastes partitus phosphoribosyl transferase domain [Gene] AND Ste ...
written 6 weeks ago by tlorin210

Latest awards to tlorin

Popular Question 3 months ago, created a question with more than 1,000 views. For Interpreting sliding windows in Ka/Ks analyses
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Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Tajima's D value interpretation
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Popular Question 14 months ago, created a question with more than 1,000 views. For Fasta to axt - KaKs Calculator
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Heatmap with categorical variables and with phylogenetic tree in R or Python
Scholar 2.0 years ago, created an answer that has been accepted. For A: Heatmap with categorical variables and with phylogenetic tree in R or Python
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