User: demoraesdiogo2017

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Posts by demoraesdiogo2017

<prev • 41 results • page 1 of 5 • next >
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Comment: A: Differences between FPKM and FPKM-UQ files in gene expression analysis
... shouldn't the quantile normalization make FPKM-UQ be suitable for cross-sample comparison? https://pubmed.ncbi.nlm.nih.gov/29112707/ here they tried different normalization methods including FPKM-UQ without finding big differences ...
written 2 days ago by demoraesdiogo201740
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Comment: C: correct way of analyzing cell proportions in singlecell data
... based, wish I could like your response 10 times If you have an article with it, please let me know so I can cite it ...
written 4 weeks ago by demoraesdiogo201740
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correct way of analyzing cell proportions in singlecell data
... Hello In Seurat there is a function to take the proportions of each cell identity so you can easily plot it with ggplots or something similar. However, most scRNA datasets I have seem (I mostly reanalyze data) have different sample sizes for each condition. So I'm sure just taking the proportions o ...
single-cell rnaseq written 4 weeks ago by demoraesdiogo201740 • updated 4 weeks ago by rpolicastro1.7k
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Comment: C: subscript out of bounds in seurat expression matrix
... this worked! thanks! ...
written 6 weeks ago by demoraesdiogo201740
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Comment: C: subscript out of bounds in seurat expression matrix
... I believe you are correct, but still when I run do heatmap using the same list of genes (DEGs$gene) with the integrated assay, the heatmap is generated. DoMultiBarHeatmap(circBALF.pred.integrated.CD4, assay = 'integrated', features = DEGs$gene, group.by='integrated_snn_res.0.5', additional.gr ...
written 6 weeks ago by demoraesdiogo201740
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Comment: C: subscript out of bounds in seurat expression matrix
... I used the RNA assay but did not specify the slot, and I assume the default is "data" additionally, when I used these genes with the Doheatmap function using the integrated data assay, many genes indeed are left out, but the heatmap is still generated ...
written 6 weeks ago by demoraesdiogo201740
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subscript out of bounds in seurat expression matrix [SOLVED]
... Hello I'm trying to build a expression matrix to use as input in a different heatmap tool used on Seurat. For that, I want to take the 500 DEGs with lowest adjusted p-value. here is what I tried: DEGs <- all.markers %>% top_n(n = -500, wt = p_val_adj) DEGs.genes <- DEGs$gene ...
seurat written 6 weeks ago by demoraesdiogo201740
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Comment: C: Merge enrichement analysis results
... Now you mention it, I think you are correct, but mostly because the enrichment scores are also calculated based on the p-values, so the enrichment of each library are likely not comparable with each other. I think it is still plausible to filter based on the false discovery rates of each database (t ...
written 3 months ago by demoraesdiogo201740
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Answer: A: Heatmap from the RNAseq raw count data
... use morpheus and never bother with any heatmap clusterization tool ever again. no coding required. https://software.broadinstitute.org/morpheus/ ...
written 3 months ago by demoraesdiogo201740
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comparing ScRNA-seq data from two different studies: should batch effects be corrected with pooled cells or not?
... Hello I would like to compare T cells from this study https://www.medrxiv.org/content/10.1101/2020.04.17.20069930v1.full.pdf with T cells from this study https://www.nature.com/articles/s41591-020-0901-9#Sec2 However, I'm not sure if I should remove batch effects from each dataset separately or wi ...
scrna-seq written 3 months ago by demoraesdiogo201740

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