User: fernardo

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fernardo 130
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Posts by fernardo

<prev • 71 results • page 1 of 8 • next >
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Comment: C: Different results between papers and GEO2R
... Even in their published work ([Paper][1]), they stated that this miRNA is down-regulated in GC patients. I believe they mixed the samples between tumor and normal when uploaded to GEO . As the others mentioned, best to check with author. [1]: https://pubmed.ncbi.nlm.nih.gov/27518872/ ...
written 4 weeks ago by fernardo 130
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Comment: C: How to get gene and microRNA expression profiles for specific type of cancers fr
... Maybe you can also use available R packages that retrieve those data e.g. "[TCGAretriever][1]" [1]: https://cran.r-project.org/web/packages/TCGAretriever/index.html ...
written 5 weeks ago by fernardo 130
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Comment: C: How to bypass WGCNA installation error?
... Update (**Solution**): I wouldn't say this would be a solution (As it still happens in R3.6), but I could manage it by installing lastest version of **R 4.0** and WGCNA could be installed easily. ...
written 5 weeks ago by fernardo 130
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How to bypass WGCNA installation error?
... I am trying to install WGCNA with R 3.6, MAC, Rstudio, and I get the following output: ``` installation of package ‘WGCNA’ had non-zero exit status ``` The first error starts by this: ``` corFunctions-utils.c:891:10: warning: unused variable 'vx' [-Wunused-variable] double vx, vy; ``` Alread ...
wgcna microarray R written 5 weeks ago by fernardo 130
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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 16 months ago by fernardo 130
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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 16 months ago by fernardo 130 • updated 16 months ago by raunakms1.1k
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Comment: C: Can this PCA be a highly good result?
... Yes, exactly, I do random sampling / bootstrapping. ...
written 16 months ago by fernardo 130
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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 16 months ago by fernardo 130
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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 16 months ago by fernardo 130
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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 17 months ago by fernardo 130

Latest awards to fernardo

Popular Question 16 months ago, created a question with more than 1,000 views. For why is this example homozygous 0/0 ?
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Popular Question 17 months ago, created a question with more than 1,000 views. For Can ncRNAs be found from all RNA-seq data?
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Can ncRNAs be found from all RNA-seq data?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Can ncRNAs be found from all RNA-seq data?
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Why GATK and bcftools SNP calling different?
Student 3.8 years ago, asked a question with at least 3 up-votes. For Why GATK and bcftools SNP calling different?

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