User: rpolicastro

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Posts by rpolicastro

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Comment: C: Problems in differential expression analysis with edgeR
... You need to also run `calcNormFactors` if you are using the glm method. ...
written 2 days ago by rpolicastro1.7k
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Comment: C: SCTransform prior or after merging samples into one object?
... Alright, I understand now. You should do SCTransform with each one separately, and then use integration to combine the separate objects. You can find more information in the 'SCTransform' tab of their [integration vignettes](https://satijalab.org/seurat/v3.0/integration.html). ...
written 3 days ago by rpolicastro1.7k
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Comment: C: Using dropEst output for Seurat
... Unless you are doing RNA velocity or have another compelling reason, you general use just the exon counts for scRNA-seq. If the data is formatted with features as row names, and cell barcodes as column names, then you can use the Seurat function `CreateSeuratObject` to start the analysis. ...
written 3 days ago by rpolicastro1.7k
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Comment: C: SCTransform prior or after merging samples into one object?
... Can you list what Seurat objects you have now, and what is in those objects? That might make it easier to understand the experimental setup. ...
written 3 days ago by rpolicastro1.7k
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Comment: C: How to run STAR with multiple files
... There should be a space between the two file names, not a comma. ...
written 4 days ago by rpolicastro1.7k
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Comment: C: Analyzing TCR clonotype in Seurat
... I can't give any specific advice because of how broad the question is, but many plotting and analysis functions will have `group.by` and `split.by` arguments that let you work with different columns in your meta-data. You can also use the `subset` function to return a seurat object that contains onl ...
written 4 days ago by rpolicastro1.7k
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Comment: C: GO terms count _ number of terms on per ontology
... Your image isn't showing up. It would also be helpful if you included some example data from your results. ...
written 5 days ago by rpolicastro1.7k
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Comment: C: Unused argument in R
... Is the function `gen.norm.dat` from a library, or did you define it elsewhere? This function is likely calling `rnorm` incorrectly, but I wouldn't be able to help without knowing the origin of the function. ...
written 6 days ago by rpolicastro1.7k
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Comment: C: How to combine p-values of differentially expressed genes from different timepoi
... What question are you trying to answer by doing this? There might be a more direct way to address it. ...
written 9 days ago by rpolicastro1.7k
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Answer: A: DESeq2- How to design data for multiple comparisons?
... I would try out two approaches. The first approach would be combining your disease subtypes and mutation factor levels for each sample. Your sample sheet would look as follows. condition sample_1 A_mut1 sample_2 A_mut2 sample_3 A_mut3 ... ... The r ...
written 9 days ago by rpolicastro1.7k

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