User: sugus

gravatar for sugus
sugus10
Reputation:
10
Status:
New User
Location:
China Pharmaceutical University
Last seen:
5 days, 17 hours ago
Joined:
1 year, 5 months ago
Email:
6********@qq.com

Posts by sugus

<prev • 18 results • page 1 of 2 • next >
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SubMap in GenePattern
... Hi there, Is anyone use GenePattern and familiar with SubMap which used to compare expression data across two data. I follow the instruction and made a label stating with 1 in 3rd line, and if there is any 0, the GenePattern will automatic add 1 to labels. However, I always get error to read cls ...
genepattern submap cls written 8 days ago by sugus10
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Comment: C: No result in enrichGO
... Yes, it works today. So weird..... ...
written 6 weeks ago by sugus10
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Comment: C: No result in enrichGO
... No, this code just makes a more decent summary, but the result is still nothing. ...
written 6 weeks ago by sugus10
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Comment: C: No result in enrichGO
... Sure, here is the contents: > de [1] "4312" "8318" "10874" "55143" "55388" "991" "6280" "2305" "9493" "1062" "3868" [12] "4605" "9833" "9133" "6279" "10403" "8685" "597" "7153" "23397" "6278" "79733" [23] "259266" "1381" "3627" "270 ...
written 6 weeks ago by sugus10
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No result in enrichGO
... Hi, I am new to clusterProfiler and following the R documentation. In the website instruction for enrichplot, here is some demo for enrichGO: library(clusterProfiler) data(geneList, package="DOSE") de <- names(geneList)[abs(geneList) > 2] ego <- enrichGO(de, OrgDb = "org.H ...
R enrichgo clusterprofiler written 6 weeks ago by sugus10 • updated 6 weeks ago by szhaoaf30
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Reorder dendrogram for a better heat map
... Hi there! I am using aheatmap to find some pattern but I need to reorder the dendrogram. I find there is a function called reorder that seems to do this job but I am really having difficulty in understanding it. I tried messing around with 'weights' for reorder, I thought when the anglo.fun = mean ...
R dendrogram reorder written 8 weeks ago by sugus10 • updated 8 weeks ago by Kevin Blighe21k
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Comment: C: How to get a matrix gene weights in NMF
... Thank you so much. It's really helpful! ...
written 12 weeks ago by sugus10
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How to get a matrix gene weights in NMF
... Hi there, Briefly, I know NMF (non-negative matrix factorization) as modeling the matrix X of expression for g genes and s samples, constituting the product of a matrix G of g gene weights for k factors and a matrix S of s sample weights for k factors. And I want to derive the matrix G for selecti ...
nmf weight matrix R written 12 weeks ago by sugus10 • updated 12 weeks ago by dariober9.1k
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(Closed) Same results using fisher.test
... Hi guys, I want to use fisher.test() to perform association analysis but I meet a confused problem. In a test data, different "alternative" will derive to different pValue > fisher.test(c(1,0,1,0,0,0,1,1,1,1,1,1),c(1,0,1,1,1,1,0,0,1,0,0,0)) Fisher's Exact Test for Count Data ...
fisher.test two-side one-side written 3 months ago by sugus10
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Error in RnBeads when customizing promoters
... Hi there, I got trouble in customizing promoters in RnBeads. I use the attached promoters2kb.R to customize a defined promoters with + - 2000kb from TSS, and set it to RnBeads. library(RnBeads) genome.assembly <- "hg19" # targeted genome assembly promoter.upstream <- 2000 ...
R promoters rnbeads written 5 months ago by sugus10

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