User: mk

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mk20
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Posts by mk

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specify a root in igraph minimum-spanning-tree
... I have a weighted adjacency matrix and I need to create a directed MST. The problem is that I know the edge weights and the root, so I can generate an MST on an undirected graph, but I cant find a way to then specify a root. If I could specify a root, this would automatically induce directions on ...
R minimum-spanning-tree directed-graph igraph written 10 days ago by mk20
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How to reproduce MATLAB tsne('algorithm', 'exact') result in R?
... Given: 1. a 25x25 matrix of integers 2. an initial 25x3 embedding, generated by PCA 3. perplexity 2 4. random seed set to 1 5. target embedding dimension 3 Run exact t-SNE using MATLAB tsne('algorithm', 'exact') and R Rtsne(theta = 0) Here is the data "A": 0 0 0 0 0 97 0 0 0 0 0 0 0 93 ...
tsne pca matlab R rtsne written 29 days ago by mk20
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Mapping Ensembl Gene IDs with dot suffix
... I have a bunch of bulk mRNA sequencing pulled off of the TCGA. Feature names appear to be Ensembl gene IDs with a suffix. Here is an example: > [995] "ENSG00000236246.1" "ENSG00000281088.1" [997] "ENSG00000254526.1" "ENSG00000223575.2" [999] "ENSG00000201444.1" "ENSG00000232573.1" I ...
gene ensembl biomart bioconductor written 6 months ago by mk20 • updated 4 months ago by PavolG0
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kmeans error when running reduceDimension(reduction_method = 'DDRTree')
... After setting my ordering filter, I run: > colonTumor <- reduceDimension(colonTumor, max_components = 3, > norm_method = c("none"), reduction_method = 'DDRTree', verbose=TRUE) Then I get the following error: > Error in kmeans(t(Z), K, centers = centers) : initial centers are not > ...
irlba monocle kmeans ddrtree written 8 months ago by mk20 • updated 8 months ago by Kevin Blighe28k
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Answer: A: Creation of cellDataSet in Monocle 2 wants undocumented AnnotatedDataFrame: assa
... turned out that fd was prepared based on a bad matrix. Issue resolved! ...
written 8 months ago by mk20
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Creation of cellDataSet in Monocle 2 wants undocumented AnnotatedDataFrame: assayData
... As directed in the [Monocle 2 Documentation][1], the cellDataSet constructor is called on a sparse matrix and two AnnotatedDataFrames. Here is the suggested usage: pd <- new("AnnotatedDataFrame", data = sample_sheet) fd <- new("AnnotatedDataFrame", data = gene_annotation) cds < ...
celldataset monocle expressionset written 8 months ago by mk20
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Processor count for cores with Intel hyper-threading in differentialGeneTest()
... The documentation for Monocle 2 discusses the use of multiple cores for differential gene expression. Will I be able to use each virtual core on a hyper-threaded processor? For instance, if I had an 8-core Xeon W, would I be able to make the following call: differentialGeneTest(, cores=14) D ...
hpc monocle hyperthreading rna-seq written 8 months ago by mk20 • updated 8 months ago by himanshuarya91620
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Given two sets of nucleotide n-mers, how can I learn sets of 'motifs' which are present in one and not the other?
... I have some unpublished data on DNA methylation, suggesting that there are differences in maintenance methylation efficiency at different sites from one cell cycle to another. I have a very coarse-grained approach for dividing the methylated sites into "likes to be methylated" and "really likes to ...
sequencing tf dna-methylation written 9 months ago by mk20
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Comment: C: Linking patient survival to gene-set analysis
... Thanks Kevin, removing the transcript suffix allowed me to map them to Entrez IDs as Ensembl genes. ...
written 9 months ago by mk20
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Comment: C: Linking patient survival to gene-set analysis
... Hi Kevin, You responses prompted me to think a bit more about what exactly I am trying to show. In particular your suggestion about clustering led me to several important works that have already been published. I've come up with a new workflow that incorporates this type of analysis, but hit one s ...
written 10 months ago by mk20

Latest awards to mk

Scholar 8 months ago, created an answer that has been accepted. For A: Creation of cellDataSet in Monocle 2 wants undocumented AnnotatedDataFrame: assa

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