User: lenC_biotecLover

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Posts by lenC_biotecLover

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rfe function from caret to perform svm-rfe feature selection
... Hi everyone, I'm trying to perform an SVM-RFE feature selection using the `caret` package on R: I have a dataset with 1000 and more features (miRNA expression counts, normalized) as columns (+ one column with the class, normal vs tumor) and few hundreds of samples as rows. I've found that the `rfe` ...
R svm caret feature selection rfe written 13 days ago by lenC_biotecLover0
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Comment: C: DESeq2: vst() and varianceStabilizingTransformation()
... Thank you very much, it is more clear now. I'm still not very comfortable with bioinformatics, so some concepts appear a bit difficult to understand for me, even if I study vignettes and documentation. ...
written 8 weeks ago by lenC_biotecLover0
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DESeq2: vst() and varianceStabilizingTransformation()
... Hi everyone, I'm exploring the `DESeq2` package, in particular the `varianceStabilizingTransformation` function. I can't completely understand the differences between this and the `vst` function: when should I use them, and why should I prefer one or the other? Thank you ...
R sva rna-seq normalization written 8 weeks ago by lenC_biotecLover0 • updated 8 weeks ago by Kevin Blighe66k
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Comment: C: DESeq2 vst function error
... I set a lower number, and it works, thank you! My dataset has 1800 miRNAs. This does mean that only few of them are considered for the calculation? How does the algorithm operates in this cases? ...
written 10 weeks ago by lenC_biotecLover0
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DESeq2 vst function error
... Hi everyone, I have a dataset with count reads of miRNA-Seq downloaded from TCGA: on the rows I have the miRNA names and on the columns the uuid barcodes(sample names). When I launch the `vst` function it gets me this error: dd = DESeqDataSetFromMatrix(d, coldata, design= ~class) vst = ...
R deseq2 rna-seq normalization written 10 weeks ago by lenC_biotecLover0 • updated 10 weeks ago by Kevin Blighe66k
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Comment: C: miRNA normalization workflow
... Ok, thank you again for the clarification. Therefore, I should correct the batch only if I find it in both my datasets (normal and tumor)? I'm sorry for all these questions, really. ...
written 10 weeks ago by lenC_biotecLover0
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Comment: C: miRNA normalization workflow
... Thank you very much for your precious advice, so RPKM is not very good to use right? ...
written 10 weeks ago by lenC_biotecLover0
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miRNA normalization workflow
... Hi everyone, I'm a biotech-student and I'm currently approaching bioinformatics and computational biology. Here are some problems I don't know how to to deal with. I have downloaded some data from TCGA, related to BRCA: miRNA quantification data, for solid tumor samples and normal samples (NAT, I k ...
normalization tcga machine learning mirna R written 10 weeks ago by lenC_biotecLover0
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Comment: C: How can I normalize RPKM data from TCGA (pan-cancer analisys)?
... I know, but I meant between the patients, considering that I've data from different projects ...
written 3 months ago by lenC_biotecLover0
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How can I normalize RPKM data from TCGA (pan-cancer analysis)?
... I have a matrix with different miRNA RPKM values downloaded from TCGA, relatively to different TCGA projects (BRCA, LAML, LUAD ecc.) columns: TCGA-barcodes, rows: miRNa identifier. In order to perform a machine learning analysis how can I normalize all this data between the patients in my matrix? ...
rpkm tcga pan-cancer rna-seq normalization written 3 months ago by lenC_biotecLover0

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