User: joseph.houjue

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Posts by joseph.houjue

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Comment: C: WGCNA with time series data
... Hi Julia, I have a similar question on my time course data. My thought is using DayX-Day0 data instead of DayX would be beneficial for avoiding the variations from individual baseline background (Day0). Do you think it's making sense? How did you do in your study? Thanks. ...
written 8 months ago by joseph.houjue0
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Comment: C: Network plot from expression data in R using igraph
... Thank you, Kevin. In order to gain separate networks at each time point, will you suggest to use DayX-Day0 as input? ...
written 8 months ago by joseph.houjue0
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Comment: A: Network plot from expression data in R using igraph
... Hi Kevin, I have a very fundamental question about how to pre-processing the time course data. In your demonstration, you have several time points, my study is also time-course data. I'm very seriously considering should we subtract the baseline (e.g. 0hr, Day0 et al) from subsequent time points pri ...
written 8 months ago by joseph.houjue0
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Minet works for time-course expression data
... I want to build up gene network from my microarray data by minet package. My data set has multi time points. If I talk about network at certain selected time point, when I give the microarray data into minet, should I use DayX - Day0 data? Any suggestion? Thanks. ...
minet time-course microarray written 8 months ago by joseph.houjue0
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Comment: C: Network plot from expression data in R using igraph
... Thanks! That sounds only indicates either identical or discrepancy without any further details. I wonder, we can make to networks, g1 and g2, the genes A, B, and C appear in both networks. Can we let them "cross-talk" vis the genes A, B, and C in the Cytoscape? or how to make two networks connected? ...
written 11 months ago by joseph.houjue0
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Comment: C: Network plot from expression data in R using igraph
... get error info as: Error in i_compare(comm1, comm2, method) : (list) object cannot be coerced to type 'double' I don't understand what's the problem. ...
written 11 months ago by joseph.houjue0
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Comment: A: Network plot from expression data in R using igraph
... Very awesome code and tutorial! I've been thinking how can I investigate the network overlap and/or uniqueness? For example, for time-course study, that'll be very interesting if looks at network "hand-shake" between two continuous time point, e.g Day3 has own network and Day4 has its own network, i ...
written 11 months ago by joseph.houjue0
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verboseScatterplot generate cor and pvalue not same as moduleTraitCor
... Dear all, I have the code as this: # Define numbers of genes and samples nGenes = ncol(VAX_Expr) nSamples = nrow(VAX_Expr) # Recalculate MEs (1st principal component) with color labels MEs0 = moduleEigengenes(VAX_Expr, moduleColors)$eigengenes # ME is the correlation matrix of modu ...
wgcna written 2.4 years ago by joseph.houjue0 • updated 2.3 years ago by Biostar ♦♦ 20
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Can I apply WGCNA on unmatched time point microarray data and clinical data
... Dear all, Usually, when I use WGCNA to make co-expression network and associated with correspond bench data. For example, A sample has -1, -2 -3 time point microarray data, and also -1, -2, -3 time point bench data(clinical data), it's usually WGCNA doing. However, some of the clinical data aren't ...
wgcna written 2.4 years ago by joseph.houjue0

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