User: qicaibiology
qicaibiology • 40
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Posts by qicaibiology
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... Hi everyone:
I am recently reading a [paper][1] on intron retention analysis, there are several places I have not figured out myself what does it mean, one example is like this:
In order to determine if an intron retention is real from the reads number among E1I(exon1intron junction), I(intron), a ...
written 4 weeks ago by
qicaibiology • 40
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... My friend and I checked the errors. What we did is : `install.packages('Matrix')`
Then we install ASpli again, and it does not show error. Going to give it a run to see what is going on.
Thanks for your help ...
written 5 weeks ago by
qicaibiology • 40
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... it does not work out in the end. I can not even library(ASpli) in the end. Looks that it still has the same problem.
"`> library(ASpli)`
> Loading required package: parallel Loading required package: edgeR
> Loading required package: limma Error: package or namespace load
> failed for ...
written 5 weeks ago by
qicaibiology • 40
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... this is what I got :
(base) [caiqi@midway2-login2 ~]$ conda activate R-3.6-env
Could not find conda environment: R-3.6-env
You can list all discoverable environments with `conda info --envs`.
(base) [caiqi@midway2-login2 ~]$ conda info --envs
# conda environments:
#
...
written 5 weeks ago by
qicaibiology • 40
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... I tried your method, and I went into R and get the following:
> library(ASpli)
Loading required package: parallel
Loading required package: edgeR
Loading required package: limma
Error: package or namespace load failed for 'edgeR' in dyn.load(file, DLLpath = DLLpath, ...):
...
written 5 weeks ago by
qicaibiology • 40
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... Thank your very much for your reply! I am trying your code to see what will happen.
Can I ask another question because I don't understand very well about it:
I saw I have anaconda2 folder and it contains lib which contains R : anaconda>lib>R, and I saw some packages in the R like edgeR and som ...
written 5 weeks ago by
qicaibiology • 40
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... Hi all:
I am working through a terminal on the computation center in the University. Recently, I need to install a package in R to analyze my RNA-seq data.
I am under the anaconda2 environment. So I use `conda install R` to install R and call R by typing `R`.
However, when I tried to install ASpli ...
written 5 weeks ago by
qicaibiology • 40
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... Thank you for your detailed and patient explanation, I modified the code according to your advice and get it work. At the same time get a deeper understanding of the comparison.
The manual I used is here ([Manual][1]) from page 7 to 8 it said when using the filter function from edgeR, it uses the C ...
written 7 weeks ago by
qicaibiology • 40
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... I ran through the steps in the manual, but get no significant changed genes. I can not figure out which part is wrong.
my code are listed as:
setwd("/Users/cqi/Desktop/kdm5bkd/")
files <- c("shCTRRep1.txt", "shCTRRep2.txt", "shKdm5bRep1.txt", "shKdm5bRep2.txt")
read.delim(files[1], n ...
written 7 weeks ago by
qicaibiology • 40
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... Thanks for your advice.
But I saw in the manual that the raw count need to be transformed into CPM?
Do you think it is not necessary?
Thanks, ...
written 7 weeks ago by
qicaibiology • 40
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