User: yifangt

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yifangt20
Reputation:
20
Status:
New User
Location:
Canada/NRC
Last seen:
3 months, 1 week ago
Joined:
3 years, 1 month ago
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y******@gmail.com

Posts by yifangt

<prev • 23 results • page 1 of 3 • next >
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How to keep track of gene names during WGCNA analysis for cutTreedynamic() and moduleEigengene()?
... I want to save the assignment of each gene on corresponding modules after cutreeDynamic(), and similarly, for merged moduleEigengenes().  I used cbind() [or merge() ] function to combine the gene names and the module/color symbols. Although in this case the order of the rows is always the same, this ...
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Comment: C: WGCNA error on block number related.
... Thank for the advice! My code are real fragment. I need more work on my code before I come back soon. ...
written 16 months ago by yifangt20
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Comment: C: Where is the "RNAseq2 level 3" data
... Thanks a lot! ...
written 16 months ago by yifangt20
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Where is the "RNAseq2 level 3" data
... I was wondering where the links are for the dataset mentioned in the CVE package in order to try the pipeline of the vignette. The dataset seems to be concatenated from the individual RNAseq2 level 3 files which is quite obscure to me. In the vignette the author stated the original dataset has been ...
concatenated tcga files rnaseq matrix written 17 months ago by yifangt20
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WGCNA error on block number related.
... When I run WGCNA according to tutorial 2.c I am stuck since this step (2.c.3: comparing single block and block-wise network analysis). The previous auto- and step-by-step analysis worked fine exactly as the tutorial instructed. Not sure what I missed with this block-wise analysis. 1) #code chunk 5 ...
wgcna subscript out of bounds block size written 17 months ago by yifangt20
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Comment: C: WGCNA with distance matrix only from newick data.
... Hello: I am still working on my distance matrix dataset (from clustalw alignment and tree creation) to get it run. adjMatrix <-adjacency.fromSimilarity(data.matrix(distMatrix), type = "distance", power = 1) Error in checkAdjMat(similarity, min, max) : some entries ...
written 17 months ago by yifangt20
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Comment: C: WGCNA with distance matrix only from newick data.
... Thanks Peter! You clarified many of my questions. First, about the trait, I have an idea to use the gene functions as trait, say, different group of transcription factors, as discrete input (without replicate etc) and, I am not sure about the adequacy at this moment either.  But, this is not my prio ...
written 17 months ago by yifangt20
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Comment: C: WGCNA with distance matrix only from newick data.
... Wrong place, and deleted! ...
written 17 months ago by yifangt20
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WGCNA with distance matrix only from newick data.
... Hello group! While I am trying WGCNA package to get modules of the candidate genes without expression data but distance matrix derived from sequence alignment. The distance matrix was converted from newick file with python script. Asking Dr Steve Horvath about this situation I was told: The WGCNA ...
wgcna hub genes eigengene written 17 months ago by yifangt20
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Comment: C: Making a circos plot to show expression for a gene set rather than whole genome
... Hello Ying: I had some difficulty to create a cir object with segAnglePo() function. My dataframe is like this one, but I always got error as > segAnglePo(seg.dat=seg.f, seg=seg.name) Error in names(x) <- value :  'names' attribute [5] must be the same length as the vector [3] Not sure wh ...
written 20 months ago by yifangt20

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Popular Question 16 months ago, created a question with more than 1,000 views. For DESeq2 RNAseq analysis with "matrix not full rank" error corrected.

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