User: ldetorrente

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ldetorrente10
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2 years, 10 months ago
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3 years, 6 months ago
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l**********@nygenome.org

Posts by ldetorrente

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Answer: A: Use of Viper with a regulatory network built with my dataset or another one?
... The maintainer of the package (Mariano J Alvarez) was actually very fast at answering emails. As maybe other people are wondering I will copy paste his answer here and hope it helps other! I would definitely use the BRCA network from aracne.networks package (bioconductor). The network should be tis ...
written 3.1 years ago by ldetorrente10
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Use of Viper with a regulatory network built with my dataset or another one?
... Hi, I am trying to use the viper package and having trouble figuring out which regulatory network I should use. Should I build one with aracne-ap directly on my dataset or better to use one from another dataset? I am working on a breast cancer dataset so my idea was to use viper with the regulator ...
regulatory network viper aracne aracne.networks written 3.1 years ago by ldetorrente10
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Comment: C: biomaRt not working anymore
... Yes, it's working again now. I'll let you know if it happens again, Thanks! ...
written 3.2 years ago by ldetorrente10
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Comment: C: biomaRt not working anymore
... I tried to change the host to www.ensembl.org and it didn't change anything. I was first trying from work and when I came back home I tried again a few hours ago and it was working (same laptop). The weird thing is that I ran my script just now and it's not working again with the same error.  ...
written 3.2 years ago by ldetorrente10
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biomaRt not working anymore
... Dear all, I am using biomaRt for a long time to map ENSEMBL ID to Gene symbol but since this morning I am getting an error and cannot make it work anymore. It's exactly the same script I was using yesterday and when I try it on another machine it works.  Thank you for your help! > library(bio ...
annotation biomart written 3.2 years ago by ldetorrente10
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Answer: A: rlog fast=TRUE not correct?
... Here are the results that you asked. Tissue_Type is my condition with 4 levels and I actually have 495 samples total (I am working on a subset at the moment). When I do an ANOVA to see the association between the size and the Tissue_Type, I have a significant p-value like you can see below.  quanti ...
written 3.4 years ago by ldetorrente10
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rlog fast=TRUE not correct?
... Hi, they finally updated the R on our cluster so I am now using DESeq2_1.10.1 with R 3.2.2.. However, I was surprised to see that the option "fast" in rlog was not available anymore, is there a reason why? Was the approximation not good/correct? I tried to run rlog in v1.10.1 but it's taking ages (3 ...
deseq2 rlog transformation vst written 3.4 years ago by ldetorrente10
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Comment: C: DESeq2 how to define my conditions when I want the results comparing a subset of
... Great, thank you so much for the help, I read your vignette 1000 times but for some reason I have skipped this part apparently.  ...
written 3.5 years ago by ldetorrente10
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Comment: C: DESeq2 how to define my conditions when I want the results comparing a subset of
... Thank you for the fast answer it helps me understand  how I can have the results for the patient-specific tissue effects. About my other question with the "remaining" samples, let's say I want to know the patient-specific tissue effects of only 3 patients Pat1, Pat2, Pat3, what do I do with the oth ...
written 3.5 years ago by ldetorrente10
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DESeq2 how to define my conditions when I want the results comparing a subset of samples
...   Hello, I am working on a large breast cancer dataset with 298 samples from 35 patients (myData). I have 3 different Tissue Type (TT1, TT2, TT3) and I saw that there was a batch effect due to the technician that did the experiment. As some of my patients have only 1 sample at the moment I am not ...
rnaseq deseq2 written 3.5 years ago by ldetorrente10 • updated 3.5 years ago by Ryan C. Thompson7.4k

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Popular Question 2.9 years ago, created a question with more than 1,000 views. For biomaRt not working anymore

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