User: ly.leifels

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ly.leifels0
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Posts by ly.leifels

<prev • 8 results • page 1 of 1 • next >
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Comment: A: what is "expression data" ?
... I wasn't sure. Thank you! ...
written 20 months ago by ly.leifels0
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WGCNA - stable Gene clustering
... I have a sample dataset derived from single cell RNA Sequencing with 1800 samples. Some genes have only few counts. Using WGCNA I can compute modules and even define the module membership for each gene for each module. I want to find the number of counts for which a gene would be safely clustered ...
wgcna written 20 months ago by ly.leifels0 • updated 20 months ago by Lluís R.810
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WGCNA "expression data": raw counts, TPM or logTMP?
... For my WGCNA analysis I need to use "expression data" for several functions. But it is not described whether this is raw count data or TPM values? Or even logTPM values? I have a scRNA Seq experiment, would it be ok to use the logTPM matrix as "expression data"? ...
wgcna expression data rna-seq written 20 months ago by ly.leifels0 • updated 20 months ago by WouterDeCoster37k
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Comment: C: Overdispersion for single cell RNA seq experiments
... for clustering genes into gene modules ...
written 21 months ago by ly.leifels0
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Overdispersion for single cell RNA seq experiments
... How can I deal with overdispersion in single-cell RNA seq experiments? especially regarding low counts? ...
scrnaseq overdispersion written 21 months ago by ly.leifels0 • updated 13 months ago by eric.kern13130
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Comment: C: TPM for low numbers of counts
... I am working with single cell RNAseq data (sorry I forgot to mention this) and I need it to be TPM values for the WGCNA ... So the gene length is known. What could I do to account for the low counts? Perhaps that one gene is very informative but it has only few counts... I want to detect for what n ...
written 21 months ago by ly.leifels0
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compare gene networks
... Hi ! I want to build different subsampled WGCNA clustered networks for gene modules. Afterwards I want to compare the subsampled networks, see if any clusters are less stable or if genes switched cluster membership. How can I compare the robustness or cluster memberships of these networks? Thank yo ...
wgcna networks written 21 months ago by ly.leifels0
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TPM for low numbers of counts
... Hi, I am trying to compute (or even deal with) the effect of low counts on TPM calculation. Is there maybe a formula or algorithm to account for this effect? TPMs strongly vary for low numbers of counts. Are there any articles or paper mentioning this problem? I couldn't find any so far... If you ...
sc rna seq tpm rna-seq written 21 months ago by ly.leifels0 • updated 21 months ago by Istvan Albert ♦♦ 79k

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