User: Edalat

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Edalat30
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Posts by Edalat

<prev • 88 results • page 2 of 9 • next >
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Comment: C: q-value or local FDR
... by metaseq package,in the end p-value is calculated as "two-sided" test,for finding DEG I want to use fdr,so I use q-value package,by this package we have q-value and local FDR,as I said after using local FDR<0.1 I don't have down-regulate genes but threshold q-value<0.1,I have some genes ...
written 3.5 years ago by Edalat30
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Input data for co-expression network by cytoscape
... hi, I need help to prepare input data for cytoscape,or recommended tutorial as a sample. For Co-Expression(Network) Analysis, I calculated correlation by R.so I have coding-non coding pairs correlation for treatment and control.now I want to draw network by cytoscape. I want molecules (genes and l ...
co-expression cytoscape rna-seq written 3.8 years ago by Edalat30 • updated 3.8 years ago by Jean-Karim Heriche24k
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Comment: C: avoid within table correlations in rcorr
... see this table that made by another person: table1 <- matrix(rnorm(25),5) table2 <- matrix(rnorm(25),5) res <- rcorr(table1, table2, type="pearson") res [,1] [,2] [,3] [,4] [,5] | [,6] [,7] [,8] [,9] [,10] # [1,] 1.00 -0.55 0.95 -0.16 0.17 |-0.46 0.15 0.10 ...
written 3.8 years ago by Edalat30
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avoid within table correlations in rcorr
... I´m building a correlation between two different matrices(coding-lncoding) with rcorr() function in R,how can I remove within table correlations?is there any way or I should remove them by hand? ...
correlation rcorr written 3.8 years ago by Edalat30 • updated 3.6 years ago by jpgsabino0
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Comment: C: warning message in rcorr function
... you have a right,it is not Intentional. no, the column was the name of sample,actually I removed that column by this function t4 <- t3[,-11] and now there is no that error. ...
written 3.8 years ago by Edalat30
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Answer: A: warning message in rcorr function
... Hi Jean, dim(coding) [1] 23 635 dim(ncoding) [1] 23 24 23 is the number of samples ,24 and 635 is the number of coding and ncoding{23 noncoding+1 column that related to myfactor(the name of samples ) & 634coding+1 column that related to myfactor} ,what is the problem? ...
written 3.8 years ago by Edalat30
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warning message in rcorr function
... hi all, when I want to calculate correlation by rcorr,the number of non coding is 23 and the number of coding is 634,R shows this warning message,what should I do? res2=rcorr(coding,ncoding,type = "spearman") Warning message: In sqrt(npair - 2) : NaNs produced I think because of Inequality of ...
correlation rna-seq rcorr written 3.8 years ago by Edalat30
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difference between meta analysis and differential expression( all treated vs all controls)
... I have a conceptional question,I have several RNA-seq experimentS (tretment /control),I did meta-analysis with expression value,on the other hand I did differential expression ( all treated vs all controls) with DEseq2. for 2 of them I should filter and select effective genes,now I want to know what ...
meta analysis deseq2 rna-seq written 3.8 years ago by Edalat30 • updated 3.8 years ago by WouterDeCoster44k
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number of genes for co-expression network
... **Hi, I did differential expression by DEseq2 for some coding and lncoding RNAseq data,this is my summery result of DEseq2 by adjusted p-value < 0.1:** **for lncoding:** out of 26998 with nonzero total read count adjusted p-value < 0.1 LFC > 0 (up) : 10, 0.037% LFC < 0 (down) : 13, ...
co-expression deseq2 rna-seq written 3.8 years ago by Edalat30 • updated 3.8 years ago by shunyip200
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Comment: C: calculate p-value for the r pairwise
... yes the number of genes in coding and noncoding are different and with this difference I calculate correlation,how can I do that?! ...
written 3.8 years ago by Edalat30

Latest awards to Edalat

Supporter 3.8 years ago, voted at least 25 times.
Rising Star 4.2 years ago, created 50 posts within first three months of joining.

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