User: xie186

gravatar for xie186
xie1860
Reputation:
0
Status:
New User
Location:
USA
Twitter:
zeamxie
Scholar ID:
Google Scholar Page
Last seen:
2 weeks, 2 days ago
Joined:
1 year, 4 months ago
Email:
x*****@purdue.edu

Posts by xie186

<prev • 10 results • page 1 of 1 • next >
0
votes
1
answers
93
views
1
answers
Comment: C: Error message by dba.plotBox() function
... Thank you.  ...
written 9 weeks ago by xie1860
0
votes
1
answers
93
views
1
answers
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 9 weeks ago by xie1860
0
votes
1
answer
93
views
1
answer
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 9 weeks ago by xie1860 • updated 9 weeks ago by Rory Stark2.1k
1
vote
1
answer
147
views
1
answer
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 8 months ago by xie1860 • updated 8 months ago by James W. MacDonald45k
0
votes
0
answers
217
views
0
answers
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 8 months ago by xie1860 • updated 8 months ago by Michael Love15k
0
votes
4
answers
794
views
4
answers
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 8 months ago by xie1860
0
votes
1
answers
337
views
1
answers
Comment: C: How to adjust the parameters of WGCNA
... Thank you so much. This is exactly what I need. I'll try this.  ...
written 9 months ago by xie1860
0
votes
1
answer
337
views
1
answer
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 9 months ago by xie1860 • updated 9 months ago by Peter Langfelder1.3k
0
votes
1
answers
300
views
1
answers
Comment: C: Subtracting INPUT reads from ChIP read counts.
... Thank you so muck for your response. Rory.  ...
written 16 months ago by xie1860
0
votes
1
answer
300
views
1
answer
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 17 months ago by xie1860 • updated 16 months ago by Rory Stark2.1k

Latest awards to xie186

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 103 users visited in the last hour