User: Guido Hooiveld
Guido Hooiveld • 2.5k
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- Wageningen University, Wageningen, the Netherlands
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Posts by Guido Hooiveld
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... Hi,
First some remarks:
Use indeed only the package `oligo` to read and process these files, and not `affy`.
There is indeed no CDF available for the HuGene ST 1.1 arrays! That's why you need the `oligo`-based framework with the corresponding PlatformDesign `(PdInfo`) info package!
gcRMA normalizat ...
written 1 day ago by
Guido Hooiveld • 2.5k
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... Thanks James, got it!
Regarding putting it on a TODO list: on one hand, for the reasons you explained above, I agree it may feel it hasn't high priority. On the other hand, because these arrays can only be processed through the `oligo` framework, and within `oligo` only the function `fitProbeLevelMo ...
written 12 days ago by
Guido Hooiveld • 2.5k
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... I noticed an intriguing discrepancy when I normalized a set of HTA2.0 arrays (GSE111156, [here][1]).
Specifically, a different number of probesets is returned when using the `rma` or `fitProbeLevelModel` function in `oligo`, even if in both cases the argument `target=core` is used. I initially notic ...
written 13 days ago by
Guido Hooiveld • 2.5k
• updated
13 days ago by
James W. MacDonald ♦ 50k
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... This has been asked here before. As far as I know Affymetrix has never released the probe information file for this array, and therefore it could not made available at Bioconductor. gcRMA normalization is thus not possible (in principle). See e.g. here: [link][1].
However, it has been suggested by ...
written 20 days ago by
Guido Hooiveld • 2.5k
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... Yes, you are correct!
`raw_data`: The assayData of this object reflect the number of probes (not probesets) present on the array. This number is independent of the 'chip definition file' (i.e. probe-to-probeset mapping) that is used. Hence these are the same for `raw_data` and `raw_data2`.
In the ...
written 22 days ago by
Guido Hooiveld • 2.5k
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... Next to the very useful case studies in the `limma` user guide, a good read to get started is also this workflow at the F1000: https://f1000research.com/articles/5-1384
Be sure to first study the case studies, though!
...
written 29 days ago by
Guido Hooiveld • 2.5k
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100
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... You didn't post your complete code, but have you assigned some IDs (probeset IDs resp. EntrezGene IDs) to the (your) 'variables' PROBEID resp. ENTREZID? I am asking because you code as such should work....(see below).
Two remarks:
I wouldn't recommend naming your variable that contains the probe/ent ...
written 10 weeks ago by
Guido Hooiveld • 2.5k
0
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1
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112
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... Please be more specific. Which rice array? There are 3 types sold by Affymetrix...
How did you normalize the data? Please provide your code.
BTW: I noticed that you tagged your post as a job advertisement, which is obviously not the case... Please remove that tag.
...
written 11 weeks ago by
Guido Hooiveld • 2.5k
0
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81
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... Thanks Martin for your hints. Using the function `description` indeed does the trick!
> description(GeneSets[[2]])
[1] "KEGG: MAPK signaling pathway"
> ...
written 11 weeks ago by
Guido Hooiveld • 2.5k
2
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... Hi,
I am using the package `GSEAbase` to import a GMT file (file with gene sets). This is working fine, but I don't understand how I can extract the 'shortDescription' of the gene sets from the `GeneSetCollection`-object. I assumed this could be done using the function `shortDescription`, but appare ...
written 11 weeks ago by
Guido Hooiveld • 2.5k
• updated
11 weeks ago by
Martin Morgan ♦♦ 23k
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