User: a.e.c

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a.e.c30
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Posts by a.e.c

<prev • 7 results • page 1 of 1 • next >
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how to combine sva with survival analysis to validate genes in an independent dataset?
... dear all, I have an RNA-seq cancer dataset for which I applied regularized Cox Regression for survival analysis ('Coxnet' from the 'glmnet' R package) obtaining 20 genes associated with survival (genes with coefficients>0). Now I would like to validate these genes with an independent dataset fro ...
coxph sva coxnet survival rna-seq written 11 months ago by a.e.c30
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Comment: C: How to account for cell type composition in differential expression analysis?
... No, I would like to adjust for different cell type composition (enrichments) in my DE analysis. I have 3 groups to compare: controls, case1, case2. ...
written 23 months ago by a.e.c30
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Answer: A: How to account for cell type composition in differential expression analysis?
... Thanks Samuel, but once I have the most variable cell types across my samples, how do I get to the gene level and find DE genes? You mention to plot a clustered heatmap with the top most variable signatures (=20-100 genes?) and then what? How do I know a gene is consistently DE within my groups? ...
written 23 months ago by a.e.c30
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How to account for cell type composition in differential expression analysis?
... Dear all, I used xCELL to obtain cell type enrichments from my bulk RNA-seq samples but now I do not know how to handle this information for a differential expression analysis. I have been investigating and one option is using CellCODE but then I do not use the information extracted from xCELL. Any ...
xcell differential expression cell type rna-seq written 23 months ago by a.e.c30
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Comment: C: Generate All Possible Permutations Of Sample Labels In R
... Obi, I am interested in applying your code above to a similar problem but instead of two groups (control and case) I have three groups (control, caseA, caseB). I would like to permute the labels of the samples across the three phenotypes and then compare control vs caseA, control vs caseB, caseA vs ...
written 2.3 years ago by a.e.c30
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Comment: C: STAR-RSEM RNA-seq pipeline is deterministic?
... But what about this from the release notes of STAR version 2.5.0a: By default, the order of the multi-mapping alignments for each read is not truly random. The —outMultimapperOrder Random option outputs multiple alignments for each read in random order, and also also randomizes the choice of the pr ...
written 2.7 years ago by a.e.c30
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STAR-RSEM RNA-seq pipeline is deterministic?
... Dear all, Do you know if STAR/RSEM are deterministic or do they have some random component to the mapping and/or quantification? Thanks, ...
star rsem rna-seq written 2.7 years ago by a.e.c30 • updated 2.7 years ago by datascientist28390

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Popular Question 22 months ago, created a question with more than 1,000 views. For STAR-RSEM RNA-seq pipeline is deterministic?

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