User: lessismore

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lessismore560
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Mexico
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Posts by lessismore

<prev • 182 results • page 1 of 19 • next >
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Comment: C: How to eliminate batch effect using removeBatchEffect function for tissue expres
... i'd rather suggest BatchQC for batch effect removal + visualization + statistics https://bioconductor.org/packages/release/bioc/html/BatchQC.html ...
written 8 weeks ago by lessismore560
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Comment: C: cannot replicate the pheatmap scale function
... Hey igor, it's the same clustering in my case because i am comparing manually scaled > pheatmap function with `scale=none` VS pheatmap scaled with `scale=rows` ...
written 11 weeks ago by lessismore560
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Comment: C: cannot replicate the pheatmap scale function
... That's the only explanation! Thanks ...
written 11 weeks ago by lessismore560
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Comment: C: Network enrichment analysis
... maybe the WGCNA paper itself will be good > https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-559 ...
written 11 weeks ago by lessismore560
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cannot replicate the pheatmap scale function
... Dear all, i am using `pheatmap` to generate some heatmaps using the function `scale=row` but i cannot replicate (at least visually, because i didn't manage to export the scaled matrix) the results if i manually scale the matrix with `t(scale (t(my.mat)))` (the scale function scales by column). Norm ...
R pheatmap written 11 weeks ago by lessismore560
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how to de-aggregate a table in R
... Dear all, i have this table. does someone know how to de-aggregate it ? plant tissue count tomato leaf 1 tomato root 4 tomato shoot 5 solanus leaf 3 solanus root 2 solanus shoot 4 what i want is a dataframe like that: leaf root shoot tomato 1 4 5 solan ...
R written 12 weeks ago by lessismore560 • updated 12 weeks ago by Chirag Parsania1.3k
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Integrate several layers of biological information to build a biological network
... Dear all, i am searching for uptodate programs/packages to integrate several data sources (e.g. RNA-Seq, metabolic, protein-protein interaction, etc.) in the same network in order to give a weight to the undirected edges based on the provenience of the gene interaction information. On the other h ...
network analysis data integration written 3 months ago by lessismore560 • updated 8 weeks ago by bharata1803390
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Rice -omics data and annotation resources
... For the rice people. As you already known there is a long list of -omics data and resources mostly in form of databases available online. Unfortunately many of them are outdated/not working/not trustable anymore. I am mainly interested in gene-gene interactions in form of co-expression, metabolic ...
rice omics ppi databases written 3 months ago by lessismore560
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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 6 months ago by lessismore560
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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 6 months ago by lessismore560

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