User: joseale2310

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joseale231010
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Posts by joseale2310

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Comment: C: How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
... Great, thank very much! ...
written 12 days ago by joseale231010
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Comment: C: How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
... I have tried a couple of things more and it seems to be the right conclusion. Thank you very much! I will try with another dataset. Just one more question, was the approach I used with DESeq2 a correct one? I mean, should I try to do the same with another dataset? ...
written 12 days ago by joseale231010
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Comment: C: How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
... I can do that but I do not quite get what implies that assumption. Thanks! ...
written 12 days ago by joseale231010
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Comment: C: How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
... I tried that but unfortunately it does not change the look of the PCA. All my samples are still completely overlapping. Isn't there then a way to modify the design to approach it in a reasonable way? I have tried to take a look at the vignettes on "Model matrix not full rank”, but it seems that my c ...
written 12 days ago by joseale231010
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Comment: C: How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
... Different early developmental stages and I want to check if how my samples reacts to a different media, that is, which stage do they seem to be closer to. I expected that at least the control should be similar to one of the downloaded dataset. Is there any other reasonable way to do this kind of com ...
written 13 days ago by joseale231010
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Comment: C: How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
... From A to F is batch 1. From G to J are my samples (2nd batch). The conditions I wrote above are simplified, but end up being the same. ...
written 13 days ago by joseale231010
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Comment: C: How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
... Hi Michael! This is the plot after. You can see a bunch of samples clustered together (G,H,I and J are my samples) https://ibb.co/gmY7CrK ...
written 13 days ago by joseale231010
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How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
... Hi! I was wondering how could I compare an RNA-seq matrix of raw counts that I downloaded from a repository to my own RNA-seq experiment. Specifically, I want to see which samples from the downloaded paper are the closest to my samples. I have tried to combine all samples into one matrix and use DE ...
limma deseq2 combat written 13 days ago by joseale231010 • updated 13 days ago by Michael Love24k

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