User: yusuf

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yusuf50
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50
Status:
New User
Location:
Norway INN
Last seen:
5 months, 1 week ago
Joined:
1 year, 7 months ago
Email:
y********@gmail.com

Posts by yusuf

<prev • 20 results • page 1 of 2 • next >
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Differential expressed genes by mix models
... Hi, I am confused with the tutorials of Gemma and Macau. I hope someone has worked with Poisson mix models - MACAU2 and Linear mix model - Gemma to process RNA-seq count data for DE genes. I am confused about why and how to get a relatedness matrix and get DE genes. I want to compare these two ...
de-genes gemma rna-seq macau written 6 months ago by yusuf50
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Answer: A: Plot read density across a normalized gene model for its each exon/intron length
... 1 - tool - http://www.iam.u-tokyo.ac.jp/nakatolab/softwares/drompa/index.html 2 - by SGA files https://ccg.epfl.ch//chipseq/doc/chipseq_tech.php 3 - paper - Wessels HH, Hirsekorn A, Ohler U, Mukherjee N. (2015) Identifying RBP Targets with RIP-seq. Methods Mol Biol 1358:141-52 ...
written 7 months ago by yusuf50
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Comment: C: deseq2 or edgeR
... after getting results I export it and then filter it by padj and logFC ...
written 9 months ago by yusuf50
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Comment: C: deseq2 or edgeR
... thanks for reply. I was filtering it after exporting to csv file. I am considering 2 fold change, so I was taking lfc 1 and pvalue 0.05 what about edgeR. ...
written 9 months ago by yusuf50
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Comment: C: deseq2 or edgeR
... I am using raw counts ...
written 9 months ago by yusuf50
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Comment: C: deseq2 or edgeR
... count from txt file for deseq2 dds <- DESeqDataSetFromTximport(count, meta, ~condition) dds <- DESeq(dds) res <- results(dds) for edger group <- factor(sample$condition) yg <- calcNormFactors(yg) design<- model.matrix(~group) yg <- estimateDisp(y ...
written 9 months ago by yusuf50
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Comment: C: deseq2 or edgeR
... so I should only consider pvalue not foldchange. what about edgeR. ...
written 9 months ago by yusuf50
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deseq2 or edgeR
... Hi, I am using DESeq2 and edgeR for my analysis. When I put cutoff of padj or FDR of 0.05 DESeq2 gives 650 DE and edgeR gives 490 DE genes But when I apply foldchange cutoff (1) also, DESeq2 give 0 DE genes and edgeR gives 352 genes. Can anyone explain to me? thanks in advance. ...
deseq2 rna-seq edger written 9 months ago by yusuf50 • updated 9 months ago by Gordon Smyth1.7k
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Comment: C: plot error x y length difference
... yup tried didn't work, but made the matrix again and it worked. ...
written 11 months ago by yusuf50
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Comment: C: plot error x y length difference
... it worked thanks :) ...
written 11 months ago by yusuf50

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