User: Teresa

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Teresa20
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Posts by Teresa

<prev • 17 results • page 1 of 2 • next >
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Comment: C: DESEQ2 design analysis
... Thanks for your repply. Just to be sure, Wouldn`t it be possible so using the counts from the healthy controls from each country to normalice the count of the samples of the same country with the condition A/B and then compare condition A and B? ...
written 5 months ago by Teresa20
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DESEQ2 design analysis
... Hi, I have done an RNA-seq experiment with samples from Spain with a condition X, samples also from Spain but healthy controls, samples from France with a condition Y and samples also from France with the condition Y. If I want to do the DEG analysis using the DESEQ2 package to know the DE genes be ...
deseq2 rna-seq written 5 months ago by Teresa20 • updated 5 months ago by WouterDeCoster40k
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Comment: C: Atypical volcano plot RNA-seq
... Thank you for your fast answer. My experiment consists in samples from two centers what I call GOE and BOL. The samples from both centers have been proccess together in the same machine, the only difference between them is that they come from different centers. As the samples from these two centers ...
written 8 months ago by Teresa20
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Atypical volcano plot RNA-seq
... Hi all, I am doing two RNA-seq analysis with unequal sample size both. In the first one, I use 10 healthy controls and 52 patients and I obtain good results when I use logFC=|2| y p-adj 0.01. Nevertheless, when I analyze the population of 7 healthy controls and 58 patients I obtain this volcano plo ...
unequal sample size deseq2 rna seq volcano-plot written 8 months ago by Teresa20 • updated 8 months ago by WouterDeCoster40k
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Comment: A: Deseq2 Etc. Unequal Sample Sizes
... Hi Devon, I am facing the same problem. I have 10 control and 48 case samples. I have used all the samples for the analysis with DESEQ2 but I obtain aprox. 3000 DE genes. I think that this high number is because of the unequal sample size. How can I deal with this situation? Is there a way to "corr ...
written 8 months ago by Teresa20
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Comment: C: Design in DESeq: Can you combine explicit and implicit batch effect correction i
... In the other thread I used the batch variable because I thought I had a batch in my dataset but I have realized that I do not have any batch. I have used another script now to generate the heatmap as you can see here: > vsd <- varianceStabilizingTransformation(ddsHTSeq, bli ...
written 9 months ago by Teresa20
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Comment: C: Design in DESeq: Can you combine explicit and implicit batch effect correction i
... I have plotted the heatmap using the dataset where I keep gender as a covariate and the top DE genes are very highlighted... One of these genes is PRKY which I have read in the literature: > > These genes are worth noting because they are all non-pseudoautosomal > X chromosome genes with ...
written 9 months ago by Teresa20
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Comment: C: Design in DESeq: Can you combine explicit and implicit batch effect correction i
... Hi Kevin, I have continued with the pipeline in the male dataset only using condition in the design and I have obtained about 1000 DE genes in the male dataset. There is a lot of difference compared to the DE genes that I obtained when using the male and female dataset joint (about 100 DE genes). ...
written 9 months ago by Teresa20
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Comment: C: Design in DESeq: Can you combine explicit and implicit batch effect correction i
... Dear Kevin, Some genes supported the hypothesis as we expected. Nevertheless, I would like to ask you if it would be a good idea separating the dataset by gender. Firstly, I would study only males from both conditions using the design ~condition. The same for females. I dont know if this is posib ...
written 10 months ago by Teresa20
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Comment: C: Design in DESeq: Can you combine explicit and implicit batch effect correction i
... Dear kevin, Sorry for the delay in my response. Thanks for the explanation. I have proceeded with this design and I have obtained 226 DE genes. Is this number too high as we should expect? Thanks! ...
written 10 months ago by Teresa20

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