User: ali.hakimzadeh

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Posts by ali.hakimzadeh

<prev • 25 results • page 1 of 3 • next >
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Comment: C: EdgeR analysis for DE genes with different time courses
... Dear [Gordon][1], for a week i try to tackle the problems of my script as you told, but with changes that you mentioned i neither could not get the DEG or maybe i did not follow the correct pathway. i plot my samples by `plotMDS(y_low)` as you advised. The results are as you see in the [Image][2]. ...
written 5 weeks ago by ali.hakimzadeh0
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Comment: C: EdgeR analysis for DE genes with different time courses
... Thanks, dear [Gordon ][1]. sorry for the late response, i catch the concept, and i will follow the commands as you told. [1]: https://www.biostars.org/u/13578/ ...
written 6 weeks ago by ali.hakimzadeh0
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Comment: C: EdgeR analysis for DE genes with different time courses
... Firstly thanks for your helpful response. I aim to design a test for pre vs. post to get DE genes. i got the filtering part [Gordon][1], but about LRT, i thought that i compare pre vs. post samples when i did `lrt<-glmLRT(fit, coef = 2:4)`, would you please explain more about that. i appreciate ...
written 8 weeks ago by ali.hakimzadeh0
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EdgeR analysis for DE genes with different time courses
... HI, I have 20 samples of leishmaniasis vaccine that all of them belong to a low dose, with four different time courses, which each has five replicate. i prepare a count table which contains gene names, and sample names with count numbers. I intend to make the identification of DE genes using a lo ...
R edger rna-seq written 8 weeks ago by ali.hakimzadeh0
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Comment: C: cuffdiff : sort order of reads in BAMs must be the same
... @benn thanks, i will try also this. indeed, you are absolutely right but i have no choices as it's my thesis. I told him in the begging when he suggests me the tophat, that these staffs are old and untrustable but he refused to accept it as he also not really into RNA-seq staff... ...
written 5 months ago by ali.hakimzadeh0
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Comment: C: cufflinks : sort order of reads in BAMs must be the same
... i know my friend but this is what my supervisor asked me to do and unfortunately i have no choice! i did it before with "edgeR" and i get the results but with cufflinks i had this problem. i want to get the 'FPKM' values so is there another tools that i can get 'FPKM' values from it? ...
written 5 months ago by ali.hakimzadeh0
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cuffdiff : sort order of reads in BAMs must be the same
... Hi all, i am trying to run cufflinks over Bam files that generated through Tophat but i get the sort order error. i lookup for other posts with this topic but they were not that much useful. I try to solve it by Samtools sort with option -n and also without it but it doesn't work. i also check the ...
cufflinks cuffdiff rna-seq written 5 months ago by ali.hakimzadeh0
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Comment: C: How to use edgeR to compare multiple conditions to reference condtiion
... that is also my question , i have the same situation but i couldn't reach the proper answer. ...
written 7 months ago by ali.hakimzadeh0
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Comment: C: analyze and compare PValues in 2 csv file by python
... thanks anyway. i didn't mean anything by "!". pardon me if you i irritate you by that. ...
written 7 months ago by ali.hakimzadeh0
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Comment: C: analyze and compare PValues in 2 csv file by python
... i saw the suggestions are toward pandas but i couldn't adopt what i want in the exercise by pandas but as it seems the only solution is to do it! the code is just to show what i use to create for my tables! that is it! ...
written 7 months ago by ali.hakimzadeh0

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Popular Question 3 months ago, created a question with more than 1,000 views. For Up/Down regulated genes list in EdgeR

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