User: ulapei
ulapei • 20
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Posts by ulapei
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... Hi,
I am trying to perform Pathway Analysis using ''Reactome PA'' package. The results I get do not include any Enriched Terms, even though it is clear that there should be some sort of associated between the pathways the genes are involved in. Whenever I try to view the data frame that contains t ...
written 19 months ago by
ulapei • 20
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... Hi,
Sorry for the simple question. I am analysing microarrays and I had to exclude a few due to the outlier detection. How do I adjust the code below, so that it recognizes that now group 1 has 6 samples and group 2 has 4 samples, instead of 7 each?
pData(eset)$Condition = rep(paste(1:2), ea ...
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... Hello!
I am trying to analyze Affy microarray data. For this, I used limma package and I noticed that I get unexpected results aka none of the genes come out as significant. After checking the p value histograms, I noticed an unusual trend - histograms appeared to be hill shaped:
![ ][1]
https ...
written 20 months ago by
ulapei • 20
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... Hi! I have tried it with MAS5. Now the plots I get are depicted below.
![https://ibb.co/gXdKJo][1]
![https://ibb.co/eiLAPT][2]
The plots seem much better, however, I still obtain that only one gene is differentially expressed.
[1]: https://image.ibb.co/jqXeJo/volcanomas5.jpg
[2]: https:// ...
written 20 months ago by
ulapei • 20
• updated
20 months ago by
andrew.j.skelton73 ♦ 5.9k
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... Yes, that is correct. I have used gcRMA normalization method to account for background background correction prior using limma. Do I need to use any other package in conjunction to gcRMA or is that enough? I have read that gcRMA works the best with Affy 3' IVT microarrays. ![enter image description ...
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... Hi Kevin,
From a bit of reading I would say that q values and p-adjusted values have a similar concept but are a bit different which makes sense because I get different values depending on the criteria I use.
For instance the output for gene x:
using 'limma', adjusted with 'fdr' yields: P.value = ...
written 20 months ago by
ulapei • 20
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... Hi,
I am trying to perform differential gene analysis using limma package along with qvalue package on several Affy microarrays. Basically I am comparing two conditions, let's say treated and untreated. I found that after running:
library(limma)
library(annaffy)
phenoData <- read.A ...
written 20 months ago by
ulapei • 20
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... Problem was solved by running R as an administrator and manually reinstalling the packages. I believe the problem was caused by several old packages that were located in only administrator accessible Temp folder. As ReacomePA could not update those packages with regular user rights, ReactomePA which ...
written 20 months ago by
ulapei • 20
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... Hi everyone,
I was wondering if anyone knows how to fix the error below:
> library(ReactomePA)
Error: package or namespace load failed for ‘ReactomePA’:
object ‘netplot’ is not exported by 'namespace:DOSE'
The answers I have found advice to uninstall and install the package. I have done so, ...
written 20 months ago by
ulapei • 20
• updated
18 months ago by
lzhizhao9179 • 0
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Answer:
A: Error with the Volcano plot
... I solved it by replacing comma with a & symbol.
> with(subset(table, logFC **>** 2.0 **&** adj.P.Val **<**.05 ), points(logFC, -log10(P.Value), pch=16, cex= c(0.4), col="paleturquoise4"))
...
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