User: xie186

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xie1860
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Posts by xie186

<prev • 20 results • page 2 of 2 • next >
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Comment: C: Error message by dba.plotBox() function
... Thank you.  ...
written 23 months ago by xie1860
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Comment: C: Error message by dba.plotBox() function
... Thanks for your reply. thrd is the threshold. I tried the latest version and I still got the message.  I sent you an email with the DBA object tamoxifen.  Shaojun  ...
written 23 months ago by xie1860
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Error message by dba.plotBox() function
... When I was using DiffBind, I got the error message below from  dba.plotBox():  Error in wilcox.test.default(toplot[[i]], toplot[[j]], paired = FALSE) :   not enough 'y' observations Calls: runDiffBind ... pv.plotBoxplot -> pvalMethod -> wilcox.test.default Could someone tell me the possible re ...
diffbind written 23 months ago by xie1860 • updated 23 months ago by Rory Stark2.8k
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How to interpret the SVA results
... I have three time courses RNA-seq data, each with 7 time points. Let's say: A0-A6, B0-B6 and C0-C6. Group A is the control. Group B and C are the treatment. Experiments were practiced in different chamber. A0, B0 and C0 should have the same expression pattern because there was no treatment. B1 and C ...
sva combat rna-seq written 2.4 years ago by xie1860 • updated 2.4 years ago by James W. MacDonald50k
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About experimental design of RNA-seq
... I have three time courses RNA-seq data, each with 7 time points. Let's say: A0-A6, B0-B6 and C0-C6. Group A is the control. Group B and C are the treatment. Experiments were practiced in different chamber. A0, B0 and C0 should have the same expression pattern because there was no treatment. B1 and C ...
wgcna block time course batch effect written 2.4 years ago by xie1860 • updated 2.4 years ago by Michael Love24k
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Comment: C: extract similar expressed genes (SEGs) rather than DEGs
... The link above doesn't work anymore. Could you please make it work again? Thanks. ...
written 2.4 years ago by xie1860
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Comment: C: How to adjust the parameters of WGCNA
... Thank you so much. This is exactly what I need. I'll try this.  ...
written 2.5 years ago by xie1860
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How to adjust the parameters of WGCNA
... I used WGCNA to construct co-expression network based on RNA_seq data from 18 samples. I got around 60 modules. Half of the modules have less than 100 genes. I selected several modules and plot the heatmap using the expression values. I found that nearly all of the modules I checked have two express ...
clustering wgcna rna-seq module co-expression network written 2.5 years ago by xie1860 • updated 2.5 years ago by Peter Langfelder2.1k
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Comment: C: Subtracting INPUT reads from ChIP read counts.
... Thank you so muck for your response. Rory.  ...
written 3.1 years ago by xie1860
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Subtracting INPUT reads from ChIP read counts.
... Hi, Recently I'm using DiffBind. After running dba.count, I can use tamoxifen$binding to get a table. > head(tamoxifen$binding)   CHR  START    END       Sample1       Sample2       Sample3    Sample4     Sample5 1   1  10400  10999  29.5902750  26.3166045  44.5083833  30.57152   2.491209 2   ...
diffbind chip-seq written 3.1 years ago by xie1860 • updated 3.1 years ago by Rory Stark2.8k

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Popular Question 11 months ago, created a question with more than 1,000 views. For How to adjust the parameters of WGCNA

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