User: Guido Hooiveld
Guido Hooiveld • 2.3k
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- Joined:
- 11 years, 9 months ago
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Posts by Guido Hooiveld
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Comment:
C: gseaplot vertical line
... Which vertical line do you exactly refer to? See here for example of a gseaplot obtained from clusterProfiler.
The calculations and interpretation of the scores can be found (among others) here (PathwayCommons) or here (at the GSEA webpage).
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written 1 day ago by
Guido Hooiveld • 2.3k
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... Please be informed that mapping of the probes to the GenCode mouse genome (release M19) has already been done by Manhong Dai from the MBNI group. The most recent version of these so-called Custom CDFs (i.e. v23) has just been released; see here and select one of the GenCode-based PdInfo (recommended ...
written 1 day ago by
Guido Hooiveld • 2.3k
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Answer:
A: Gene names for the Probes
... Check this thread here: https://support.bioconductor.org/p/89308/
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written 5 weeks ago by
Guido Hooiveld • 2.3k
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... Thanks for the pointers; got it working.
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written 6 weeks ago by
Guido Hooiveld • 2.3k
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... Hi,
I have a list of Gene Ontology IDs, and I would like to extract the genes (ensembl IDs) that belong to these GO terms. To do this I would like to use the biomaRt package. However, I cannot get it to work; i get an error indicating an invalid filter is used. This also happens when running an exa ...
written 6 weeks ago by
Guido Hooiveld • 2.3k
• updated 6 weeks ago by
James W. MacDonald ♦ 48k
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Comment:
C: OrgDb for Tetrahymena thermophila
... Well, the above line of code (still) works for me on the current version of R/BioC... (although run-time was longer than before [now ~20hrs]). If needed, I can sent you the OrgDb library I made.
># set working dir to a location with sufficient HDD space
># needed >35GB
>setwd("D:\\my ...
written 7 weeks ago by
Guido Hooiveld • 2.3k
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... "The first column, baseMean, is a just the average of the normalized count values, dividing by size factors, taken over all samples."
See e.g. Mike's workflow published at the F1000 here (section "Building the results table").
...
written 8 weeks ago by
Guido Hooiveld • 2.3k
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... FYI: Johannes' solution is automagically performed within the tximport function when specifying the argument ignoreTxVersion = TRUE (default = FALSE).
...
written 8 weeks ago by
Guido Hooiveld • 2.3k
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... at the help page of ReadAffy (found by ?ReadAffy) find the option 'compress':
compress: are the CEL files compressed?
Thus (assuming the last file in your list (GSM1293830_19_10_Control_108h.CE) has a wrong extension because of an incomplete copy/paste error):
AffyData <- ReadAffy(filenam ...
written 10 weeks ago by
Guido Hooiveld • 2.3k
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... Your code is working for me. I used as input the 12 UMA IDs above.
Although not directly related to the problem your reported, please note that the function enrichKEGG() is used to check which KEGG pathways are over-represented in a list of selected genes, e.g. identified by an differential gene ex ...
written 11 weeks ago by
Guido Hooiveld • 2.3k
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For A: clusterProfiler: Which GO version is used behind ?
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