User: lessismore

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lessismore490
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Posts by lessismore

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Comment: C: Visualizing model-based clustering with fviz_mclust
... Thanks Kevin. Given your expertise in this could you tell me if you know why some objects of the same cluster are not in the same circle? What does that mean? ive seen that they might have a lower probability to belong to the cluster and that's ok, but why the circle doesnt include them? ...
written 25 days ago by lessismore490
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Comment: C: Visualizing model-based clustering with fviz_mclust
... Thanks kevin, could you please tell me or point me to a link where it's showed how to implement it? ill try to remember it for the rest of my life! ...
written 26 days ago by lessismore490
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Visualizing model-based clustering with fviz_mclust
... Dear all, i have data matrix with samples on rows and genes on columns. i am using `fviz_mclust` function in `factoextra` package as explained here > http://www.sthda.com/english/articles/30-advanced-clustering/104-model-based-clustering-essentials/ When plotting the clusters with this functi ...
factoextra clustering written 26 days ago by lessismore490 • updated 26 days ago by Kevin Blighe24k
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Comment: C: fviz_nbclust (kmeans) with method "gap_stat" error: did not converge in 10 itera
... > dim(df) [1] 2068 25 Im using the default parameters: fviz_nbclust(df, FUNcluster = MyKmeansFUN, method = "gap_stat", diss = NULL, k.max = 10, nboot = 100, verbose = interactive(), barfill = "steelblue", barcolor = "steelblue", linecolor = "steelblue", print.summary ...
written 4 weeks ago by lessismore490
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Comment: C: fviz_nbclust (kmeans) with method "gap_stat" error: did not converge in 10 itera
... Dear Kevin, thanks a lot for your help. Do you have any idea about what this means? > fviz_nbclust(df, FUNcluster=MyKmeansFUN, method="gap_stat") Clustering k = 1,2,..., K.max (= 10): .. done Bootstrapping, b = 1,2,..., B (= 100) [one "." per sample]: ............... ...
written 4 weeks ago by lessismore490
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fviz_nbclust (kmeans) with method "gap_stat" error: did not converge in 10 iterations
... Dear all, im trying to find the optimum number of clusters to fit to a gene expression dataset. For this, Im using the packages `FactoMineR` and `factoextra` and the function `fviz_nbclust` on my scaled dataframe (simple dataframe with genes in rows and samples in columns). It scales (z-sc ...
kmeans clustering written 5 weeks ago by lessismore490 • updated 5 weeks ago by Kevin Blighe24k
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Comment: C: Deep exploration of an expression atlas
... Thank you very much, ive been looking at genefilter, precisely to this: varFilter(as.matrix(my_expression_data), var.func=IQR, var.cutoff=0.6, filterByQuantile=TRUE) from what ive read, it calculates the interquartile range of each gene, then it sorts the values and it takes the ones above t ...
written 10 weeks ago by lessismore490
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Comment: C: Deep exploration of an expression atlas
... My aim would be focusing on genes with interesting (preferred) expression changes to be useful for prediction purposes ...
written 10 weeks ago by lessismore490
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Deep exploration of an expression atlas
... Dear all, i want to deeply analyse an expression compedium. A part from the classical methods such as 1. plotting for each sample expression distribution via boxplot or density plots 2. clustering via PCA 3. producing expression heatmaps i would be interested in other solutions that wou ...
R data exploration rna-seq written 10 weeks ago by lessismore490
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Redundant gene list simplification
... I need to convert this format: TMCS09g1008676 fleshy 0.000234939 TMCS09g1008676 fleshy 1.38379E-05 TMCS09g1008676 fleshy 0.00331883 TMCS09g1008677 fleshy 0.0481578 TMCS09g1008678 fleshy 0.0350491 TMCS09g1008679 fleshy 0.0335639 TMCS09g1008680 fleshy 0.0167087 TMCS09g ...
R awk written 11 weeks ago by lessismore490 • updated 11 weeks ago by EagleEye5.5k

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