User: wt215

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wt2150
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Posts by wt215

<prev • 8 results • page 1 of 1 • next >
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Comment: C: bplapply with progressbar
... Thank you Martin! Is it possible to allow bplapply for passing arguments to the function txtProgressBar? If so then I can specify 'max=10000', so that progress bar will be element based. For this toy example, rowMeans definitely works better. i just used it for illustration. By the way, BiocParall ...
written 4 weeks ago by wt2150
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bplapply with progressbar
... Hello, I am replacing foreach with BiocParallel in my package. I wonder whether could I maintain the same setting of progress bar  as in foreach for bplapply. (The same problem as listed in https://github.com/Bioconductor/BiocParallel/issues/54 and https://stat.ethz.ch/pipermail/bioc-devel/2017-Dec ...
bplapply progressbar written 4 weeks ago by wt2150 • updated 4 weeks ago by Martin Morgan ♦♦ 22k
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Comment: C: is SCEset fully abandoned in scran?
... Hi Davis, Thanks , I see. How about your paper "A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor", will you also update the code in that paper in the future?  Many thanks! Best wishes, Wenhao ...
written 13 months ago by wt2150
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is SCEset fully abandoned in scran?
... The function "newSCEset()" is convenient, but I just realized that this function is deprecated. Does this mean that "SCE" is fully abandoned and now we turn to "SingleCellExperiment" for storing our scRNAseq data?   Thank you very much!   ...
normalization scran scater splatter written 13 months ago by wt2150 • updated 13 months ago by davis90
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Comment: C: apply edgeR TMM normalization without converting data format into 'DGEList'
... Thank you very much! That's very helpful! ...
written 22 months ago by wt2150
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Comment: C: apply edgeR TMM normalization without converting data format into 'DGEList'
... Sorry, I thought the downstream analysis involves DE analysis and clustering or any statistical methods. I thought that once we obtained a normalized count table, we can apply any statistical methods on it.  ...
written 22 months ago by wt2150
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apply edgeR TMM normalization without converting data format into 'DGEList'
... Hi, I would like to apply edgeR TMM normalization without converting data format into "DGEList", in other words I would like to manipulate the raw count table. (By doing so I can get a feeling about the whole RNAseq analysis procedure). May I ask that if I just do the following: (Raw count table) ...
edger tmm normalised values written 22 months ago by wt2150 • updated 22 months ago by Gordon Smyth35k
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Comment: C: edgeR TMM values
... Hi Aaron, may I ask a relevant question here? If I just do: (Raw count table)*(norm.factor), where norm.factor=edgeR::calcNormFactors((Raw count table),method='TMM'). And then conduct downstream analysis. Does this procedure make sense? After downstream analysis, can I say that I applied TMM met ...
written 22 months ago by wt2150

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