User: Maya

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Maya0
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Posts by Maya

<prev • 34 results • page 1 of 4 • next >
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Comment: C: How to interpret a Scree plot
... Hi, thank you for your answer! These are 2 plot from plotPCA function from the DESeq2. A batch that I could consider is the different days of library preparation (e.g Date1 and Date2). ...
written 5 weeks ago by Maya0
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Comment: C: Interpretation of PCA plot
... Ok thank you very much for your suggestions! ...
written 5 weeks ago by Maya0
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Comment: C: Interpretation of PCA plot
... Thank you for your answer. This is the plot by date only. What do you mean with "look at further dimensions"? ...
written 5 weeks ago by Maya0
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Comment: C: Interpretation of PCA plot
... I was hoping that someone could answer your statement by looking at the plot ,if possible, I mean how can I understand the meaning of the cluster? The batch that I could consider could be the different days of library preparation (e.g Date1 and Date2 in the plot). ...
written 5 weeks ago by Maya0
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Interpretation of PCA plot
... Hi to all, I obtain this plot after vst method of DESeq2. Should I proceed with batch effect correction or my data are good without also without the correction? Sorry for my question but I'm not sure how to interpret this plot. Thank you in advance for any suggestion! ...
rna-seq written 5 weeks ago by Maya0
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Comment: C: How to interpret a Scree plot
... Thank you for your very clear explanation. Actually I have a total of 60 samples: 30 tissues from one in individual and 30 from another one (e.g liver1 and liver2, lung1 and lung2 and so on). > What your scree plot is telling you is that you have roughly 4-7 PCs that may be of interest in your d ...
written 6 weeks ago by Maya0
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How to interpret a Scree plot
... Hi to all, I'm working with RNA-seq data and I 'm trying to figure out if in my data there is a batch effect. I normalized my data in TPM through Salmon and then I run the following code > setwd("~/R") > countData <- read.csv("CountData.csv",row.names="X") &g ...
rna-seq written 6 weeks ago by Maya0 • updated 6 weeks ago by rpolicastro3.2k
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Comment: C: How to evaluate gene expression
... Probably it is a stupid question so sorry. But is it possible to compare A vs B,C,D and so one in the same time or is it necessary to compare A vs B, then A vs C and so on? ...
written 6 weeks ago by Maya0
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Comment: C: How to evaluate gene expression
... Actually I'm not working with 2 different tissues but with a lot. For each tissue of an individual I have the biological replicate of the same tissue in the other individual. I don't know if I have a consistent batch effect because the procedures (e.g. poly-A selection, library preparation etc.) wer ...
written 6 weeks ago by Maya0
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Comment: C: How to evaluate gene expression
... Thank you for you answer but I think that there is a statistical way to establish like a sort of cut-off above which we can consider that a particular gene is expressed. I mean, why TPM>1? Reading throughout different posts I realized that we cannot establish a cut-off (e.g. TPM>1) in a rando ...
written 6 weeks ago by Maya0

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