User: TriS

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TriS3.1k
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Posts by TriS

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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... looks like you don't have a columns called patient.bcr_patient_barcode or it's empty, therefore you can't assign it to the variable you are creating. ...
written 4 weeks ago by TriS3.1k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... check class(clinical) if it's a matrix, transform it into a data.frame ...
written 6 weeks ago by TriS3.1k
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Comment: C: Concatenate RNA-seq technical & biological reps or just technical reps before al
... for DE transcripts keep the biological replicates separated, align them separately and then calculate DETs/DEGs. for SNPs I'd suggest to do a similar approach. call SNPs per each replicate and keep those common across biological replicates. ...
written 10 weeks ago by TriS3.1k
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Comment: C: DESeq2 Heatmap issue
... figure margins too large make the figure smaller and try again png("qc-heatmap-samples.png", w=500, h=750) ...
written 11 weeks ago by TriS3.1k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... this should be posted as a new question since it's not specific for this tutorial. anyhow..1) how does `head(rna)` look? 2) it seems you don't have a design matrix `d` 3) how many genes are in `rna`? ...
written 3 months ago by TriS3.1k
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Comment: C: Is there a way to calculate p-values, FDR or t test starting from logFC data?
... you don't need raw count values, you can use TPM and limma to get DEGs ...
written 3 months ago by TriS3.1k
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Answer: A: Is there a way to calculate p-values, FDR or t test starting from logFC data?
... it's a (partial) duplicate question from here: https://www.biostars.org/p/248383/ here https://www.biostars.org/p/8945/ see answers there. also from Google: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4728800/ https://www.bioconductor.org/help/workflows/rnaseqGene/ http://biocluster.ucr.edu/~r ...
written 3 months ago by TriS3.1k
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Answer: A: B Cell Epitope Prediction: Maximizing Antigenicty and Minimizing Sequence Lengt
... immunogenicity prediction is a very uncharted territory. that is, a potential antigenicity (or peptide recognition by the MHC) still does not tell you whether your lymphocytes have the receptor's repertoire (TCR or BCR) to recognize the peptide. this means that once you move into in vitro and in viv ...
written 3 months ago by TriS3.1k
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Answer: A: CPM and FPKM value
... simple and to the point, thank you Google: https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/ ...
written 3 months ago by TriS3.1k
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Comment: C: secondaryFiles for bam: how to handle .bai or/and ^.bai ?
... are you trying to get the files that end with either bam.bai or .bai? if that's the case just grep out those with .bai.... how are your writing your workflow? unix shell? ...
written 3 months ago by TriS3.1k

Latest awards to TriS

Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Commentator 9 weeks ago, created a comment with at least 3 up-votes. For C: Diagnose my daughter?
Scholar 3 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Diagnose my daughter?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Scholar 4 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Popular Question 4 months ago, created a question with more than 1,000 views. For pros- and cons- : programming skills vs. GUI
Popular Question 5 months ago, created a question with more than 1,000 views. For pros- and cons- : programming skills vs. GUI
Scholar 6 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Popular Question 6 months ago, created a question with more than 1,000 views. For pros- and cons- : programming skills vs. GUI
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: How to check whether two genomic regions contact in 3D?
Popular Question 7 months ago, created a question with more than 1,000 views. For pros- and cons- : programming skills vs. GUI
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: How to check whether two genomic regions contact in 3D?
Appreciated 10 months ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Appreciated 10 months ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Scholar 11 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Epic Question 14 months ago, created a question with more than 10,000 views. For Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Popular Question 14 months ago, created a question with more than 1,000 views. For sample size, normality assumption, t.test/anova for DEG analysis
Gold Standard 15 months ago, created a post with more than 25 bookmarks. For Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Popular Question 17 months ago, created a question with more than 1,000 views. For TCGA survival analysis with z-scores all samples altered
Popular Question 17 months ago, created a question with more than 1,000 views. For TCGA survival analysis with z-scores all samples altered
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: How to check whether two genomic regions contact in 3D?

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