Question: analyze and compare PValues in 2 csv file by python
0
gravatar for ali.hakimzadeh
3 days ago by
ali.hakimzadeh0 wrote:

Hi all,

I am doing an RNA-seq analysis. I have two CSV files, and I want to get a set of data of my genes during P Values to know which genes in each CSV file are up regulated. EdgeR achieves the tables in differential gene expression in R studio, and the script is written down. I use the codes for both tables that I have for gene counts achieved by ht-seq. At frist i want to know which genes are common among two tables and then use a python script to build a set or table to tell me which genes in each table are up regulated and which are not from the mutual ones that i find. The P value that i consider is < 5% . How can I do it by python? Also there is a point that i have to mention that the genes orders(first column) in the tables are not the same and they are different!

library(edgeR)

group <- factor(c(rep("pro-vaccine",30),rep("pre_vaccine",20)))
x<-read.csv("table_50_ID.csv")
y<-DGEList(counts = x, group=group)
y<-calcNormFactors(y)
design<-model.matrix(~group)
y<-estimateDisp(y,design)
fit<-glmFit(y,design)
lrt<-glmLRT(fit,coef = 2)
deg <-topTags(lrt, n = Inf , p= 0.05)$table
up <-deg[deg$logFC > 0,]
down <-deg[deg$logFC < 0,]
write.csv(up, file="up.csv")
write.csv(down, file="down.csv")

Here is also my tables shapes in R studio:

table

Thanks in advance

rna-seq csv python • 73 views
ADD COMMENTlink modified 3 days ago • written 3 days ago by ali.hakimzadeh0

Why do you need to use python? If you're reading files into R, why not use R to compare columns of a data.frame to achieve what you need?

ADD REPLYlink written 3 days ago by RamRS21k

the problem is i am not a R programmer and i am not into that! i just use this package because i am stimulating an article process! that is also why i want to compare two tables which is mine and them!

ADD REPLYlink written 3 days ago by ali.hakimzadeh0

In that case, I'd recommend you read up on pandas and use that to compare/manipulate your datasets.

https://pandas.pydata.org/

Also, in this case, the R code you supplied has nothing to do with the exercise, as you merely need to understand how to work with tabular data/CSV files in python.

ADD REPLYlink modified 3 days ago • written 3 days ago by RamRS21k

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!

ADD REPLYlink written 3 days ago by ali.hakimzadeh0

Yes, you're going to have to learn one technology or the other.

A side note: Use the ! mark judiciously. It can make sentences appear quite prickly when used improperly or overused.

ADD REPLYlink written 3 days ago by RamRS21k

thanks anyway. i didn't mean anything by "!". pardon me if you i irritate you by that.

ADD REPLYlink written 3 days ago by ali.hakimzadeh0

No problem, it's just quirks with language usage.

ADD REPLYlink written 3 days ago by RamRS21k
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