User: Sib
Sib • 20
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- 10 months, 3 weeks ago
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Posts by Sib
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... Thanks for your answer.
We want to introduce new blood candidate biomarkers for one disease. We hypothesize that novel and potentially more specific biomarkers in the blood could be identified by searching for disease-associated pathways that overlap between cells in the peripheral blood and the inf ...
written 23 days ago by
Sib • 20
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... I performed a differential expression analysis of microarray and RNAseq datasets between healthy control samples and patient samples and obtained a list of differentially expressed genes. Now, I want to find upstream regulators of these DEGs. I am seeking a tool or platform that does this for free. ...
written 23 days ago by
Sib • 20
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Comment:
C: How can I put the Rtools on PATH?
... Yes. I saw that but my problem is that I don't understand the meaning of this:
You can do this with a text editor, or you can even do it from R like so:
writeLines('PATH="${RTOOLS40_HOME}\\usr\\bin;${PATH}"', con = "~/.Renviron")
when I copy and paste this line in R
writeLines('PATH="${RTOO ...
written 4 months ago by
Sib • 20
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... I Installed the last version of R. Now when I use install.packages function, it gives me this warning:
>install.packages("limma")
Warning in install.packages :
unable to access index for repository https://cran.rstudio.com/src/contrib:
cannot open URL 'https://cran.rstudio.c ...
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278
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... Where are the method section and metadata? ...
written 9 months ago by
Sib • 20
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... No these are two different questions. I want to analyze microarray data in R. Now I want to know if I get the datasets by getGEO I should perform background correction and substitution of duplicates with the mean or like GEO2R not. ...
written 9 months ago by
Sib • 20
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... getGEO function is a way of getting datasets and their annotations from GEO in R when we want to analyze microarray data.
GEO2R uses this function to get datasets. I saw in the GEO2R scripts of many of GEO cases that the tool does not perform background correction and substitution of duplicates wit ...
written 9 months ago by
Sib • 20
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... Thanks for your answer. Can we say whenever we obtain datasets by using getGEO function, the data are background corrected and duplicates are substituted with mean, and even if we want to have our analyze by R (without GEO2R), if we get datasets through this function there is no need to background c ...
written 9 months ago by
Sib • 20
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526
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... The commands below are the R scripts that are used to analyze my microarray data. I want to know which lines are responsible for
1-Replacing replicated probes with the mean
2-Background correction
# Differential expression analysis with limma
library(Biobase)
library(GEOquery)
...
written 9 months ago by
Sib • 20
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... I already have up-voted to the answer and ticked accept and after that, I deleted the post because I thought that it was not useful for the entire community. ...
written 10 months ago by
Sib • 20
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created a question with more than 1,000 views.
For How can I put the Rtools on PATH?
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