User: yueli7

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yueli70
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Posts by yueli7

<prev • 24 results • page 1 of 3 • next >
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Comment: C: chippeakanno annotation
... The following code snippets might fit your needs. library(TxDb.Hsapiens.UCSC.hg38.knownGene) TxDb <- TxDb.Hsapiens.UCSC.hg38.knownGene TSS <- genes(TxDb) exons <- exons(TxDb) fiveUTRs <- unique(unlist(fiveUTRsByTranscript(TxDb))) threeUTRs <- unique(unlist(threeUTRsByTranscri ...
written 16 days ago by yueli70
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chippeakanno annotation
... Hello, I tried to use "TxDb.Hsapiens.UCSC.hg38.knownGene" to annotate my peaks by ChIPpeakAnno 3.16.1. My question is how I can annotate each peaks whether it is exon, intron, 3'UTR, 5'UTR or in promoter region? Thanks! yue ...
annotation written 16 days ago by yueli70
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Comment: C: want the piece of the matrix I wanted
... Avel Klenk,   Thank you so much for your great help!       > library("Hmisc") Loading required package: lattice Loading required package: survival Loading required package: Formula Loading required package: ggplot2 Attaching package: ‘Hmisc’ The following objects are masked from ‘package: ...
written 12 months ago by yueli70
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want the piece of the matrix I wanted
... Hello,   I only want a piece of the matrix, not the whole.   I only want the fifth column to the end and the first row to the fourth.   That means I only want   P V1 V2 V3 V1 0.3506 0.2943 0.6931 V2 0.7733 0.0383 0.8874 V3 0.4476 0.2438 0.0652 V4 0.1597 0.6114 0.6958     Thanks in ad ...
matrix written 12 months ago by yueli70 • updated 12 months ago by Axel Klenk920
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rcorr problem of Hmisc package
... Hello,   I try to calculate the correlation of P value of two matrix. Thanks in advance!       > library("Hmisc") > x<-as.matrix(read.table("tmp01")) > x      V1 V2 V3 V4 V5 [1,]  1  2  3  4  5 [2,]  4  1  6  5  1 [3,]  3  5  5  2  2 [4,]  1  2  3  4  5 [5,]  4  1  6  5  1 > y& ...
software error hmisc written 12 months ago by yueli70 • updated 12 months ago by shepherl ♦♦ 1.4k
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Comment: C: edgeR and DESeq2
... Thanks, Gordon Smyth, What is the mean of "IMO "? Thank you! ...
written 13 months ago by yueli70 • updated 13 months ago by Gordon Smyth37k
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edgeR and DESeq2
... Hello, I used the edgeR and DESeq2 to calculate the differentially expressed genes. Of course, the results are not identical. I read many papers, and both of the packages are evaluated quite good. My question is, what I can do? Is that possible I can get the intersection or the union of the data ...
edger deseq2 written 13 months ago by yueli70 • updated 13 months ago by Gordon Smyth37k
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how to calculate the logFC value
... Hello, I used edgeR. After calcNormFactors, I got the norm.factors, then I tried to use the counts number and norm.factors to calculate the logFC. 1. (478/1.0296636+619/1.0372521+628/1.0362662+744/1.0378383)/4=596 (483/0.9537095+716/0.9525624+240/0.9583181)/3=503 log2(503/596)=-0.244754 2. (47 ...
edger written 13 months ago by yueli70 • updated 13 months ago by Gordon Smyth37k
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Answer: A: calculate foldchange after rlogTransformation
... Thank you so much for your great help! ...
written 13 months ago by yueli70
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calculate foldchange after rlogTransformation
... Hello, I have human lung cancer cell data with no replicates, and following all the procedures in DESeq2. After rlogTransformation, I got this table: rld<-rlogTransformation(dds2),     X549_repair.bam X6_repair.bam X6plus_repair.bam X14_repair.bam X14plus_repair.bam ...
deseq2 written 13 months ago by yueli70

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Popular Question 3.9 years ago, created a question with more than 1,000 views. For install RCurl in R

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