User: salamandra

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salamandra170
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Posts by salamandra

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Comment: C: Tool that can split genes into groups with similar expression pattern overtime
... thank you very much! ...
written 27 days ago by salamandra170
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Comment: C: Tool that can split genes into groups with similar expression pattern overtime
... You're talking about distance matrix? I know I can use to visualize those groups in a heatmap, but then how to aftwrwards automatically get the list of genes in each group/branch separately? I have a lot of genes so cannot do it manually ...
written 28 days ago by salamandra170
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Comment: C: Tool that can split genes into groups with similar expression pattern overtime
... Yes, the thing is to know which genes are in the same group. Each plot shows a group of genes with the same behaviour through time ...
written 28 days ago by salamandra170
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Tool that can split genes into groups with similar expression pattern overtime and plot them?
... Does anyone know of a tool that can produce similar plots to 'DegPatterns' function of 'DEGreport' R package? something like this [plot][1]? Basically is a plot showing how groups of genes change over time. Cause I'm having difficulties with DegPatterns. [1]: https://github.com/hbctraining/DGE ...
rna-seq clustering written 28 days ago by salamandra170 • updated 28 days ago by exin30
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degPatterns: Error in lower.to.upper.tri.inds(n) : 'n' must be >= 2
... When running this: clusters <- degPatterns(cluster_rlog, metadata = TableBJ, time = "condition", col=NULL) I get this error: Error in lower.to.upper.tri.inds(n) : 'n' must be >= 2 and also get a warning: Large number of genes given. Please,make sure is not an error. NormallyOn ...
rna-seq clustering written 29 days ago by salamandra170
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Comment: C: Deseq2: What is the most correct experimental design for this experiment?
... thank you :) I'm not sure, as I haven't done it. I'll just play safe and work with each combination of time and celltype, intead of time alone or cell type alone ...
written 4 weeks ago by salamandra170
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Comment: C: Deseq2: What is the most correct experimental design for this experiment?
... The experience consists in converting one cell type in the other. So, at different time points of the process we did rna_seq. Celltype is the phenotype we observed. So for one of the time points we observed two phenotypes and variance was big and for two other time points which shared same phenotype ...
written 4 weeks ago by salamandra170
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Comment: C: Deseq2: What is the most correct experimental design for this experiment?
... And simply removing time of the table/design wouldn't be correct? I ask because most of variance in PCA plot (PC1 and PC2) is due to cell type. Not even in PC2 and PC3 time seems to vary. ...
written 4 weeks ago by salamandra170
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Comment: C: Deseq2: What is the most correct experimental design for this experiment?
... I'm having problems in understanding confounding variables, because imagine this situation: time <- factor(LETTERS[1:4]) celltype <- factor(c(1,2,2,3)) sampleNames <- c("hey","hi","HRY", "GT") sampleFiles <- c("1A_ATCACG_counts", "2A_CAGATC_counts", "3A_ATCACG_counts", " ...
written 4 weeks ago by salamandra170
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(Closed) Updated R and now can't install package "DEseq2"?
... I updated R to version 3.5 because I couldn't install package 'tibbles', but now the package I need the most 'DEseq2' is not installed. I tried to install with source("https://bioconductor.org/biocLite.R") biocLite() biocLite("DESeq2") and with install.packages("DESeq2") and i ...
R version install deseq2 packages written 4 weeks ago by salamandra170

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