User: fernardo

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fernardo 120
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Italy
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2 years, 12 months ago
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Posts by fernardo

<prev • 67 results • page 1 of 7 • next >
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Comment: C: How to check if first two components of PCA are separated without visualisation?
... Thanks a lot. It seems a solution to me. I am going to try that. But to fully understand your point: 1- in-class distance: do you mean to calculate pairwise correlation between PC1 and PC2 for a condition(class) ? 2- out-class distance: this one related to first point and didn't get it actually ...
written 3 days ago by fernardo 120
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How to check if first two components of PCA are separated without visualisation?
... Hi Everyone, In the following examples we see the second example has better result and more separable. Is it possible to see somehow **find this separation based on the data matrix of PCA result**? e.g. based on some kind of score like Mean, Median calculation of the components or any other way? ...
R ngs pca machine learning python written 4 days ago by fernardo 120 • updated 3 days ago by raunakms990
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Comment: C: Can this PCA be a highly good result?
... Yes, exactly, I do random sampling / bootstrapping. ...
written 9 days ago by fernardo 120
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Comment: C: TCGA metastatic samples
... Actually I have seen the same situation, too. It is not exactly non but most of the cancer data that I also downloaded from firebrowse contains only a few or non-metastatic (code 06) samples. ...
written 10 days ago by fernardo 120
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Comment: C: Can this PCA be a highly good result?
... Two answers are here. First, if a subset of gene gives me the same output as the entire dataset, why is it not useful and scientific with less effort and information, gives good and same result? what do you think? Second, following what others generally do like DE analysis and heatmap is not man ...
written 10 days ago by fernardo 120
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Comment: C: Can this PCA be a highly good result?
... @Devon and @Kevin, thanks for both. I am picking up genes randomly and most of them are not differentially expressed or at least not statistically significant in that term. So my point is that, perhaps among those 20 genes only 3 of them differentially expressed and make such out. Can this be signif ...
written 12 days ago by fernardo 120
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Comment: C: Can this PCA be a highly good result?
... Thanks. The study is from two conditions (disease vs normal). ...
written 12 days ago by fernardo 120
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Comment: C: Is it fine to run SVM on RNA-seq read counts?
... Here is one outcome of SVM on the data. ...
written 12 days ago by fernardo 120
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Comment: C: Can this PCA be a highly good result?
... Actually I asked a question not trying to answer one :) thanks for the link too. ...
written 12 days ago by fernardo 120
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Can this PCA be a highly good result?
... Hello All, Can somebody please tell me if this PCA result but a good result and which way recommended best to validate that? Note: the PCA is based on around 20 features and the samples are around 100. ![enter image description here][1] Thanks a lot [1]: https://i.ibb.co/TLN6g8S/pcabio ...
ngs pca machine learning rna-seq written 13 days ago by fernardo 120

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Popular Question 4 weeks ago, created a question with more than 1,000 views. For Can ncRNAs be found from all RNA-seq data?
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