User: Guido Hooiveld
Guido Hooiveld • 2.5k
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Posts by Guido Hooiveld
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... Your lines of code worked fine for me when starting directly from a set of raw data (CEL) files. This means that your input data (i.e. `set8`) was somehow wrong... Assuming you would like to use the expression data in the Series Matrix File available at GEO, I would recommend to use functions from t ...
written 5 days ago by
Guido Hooiveld • 2.5k
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... I irregularly use this library. If I recall correctly, I had to change few lines of code to get it working. I also do not use the built-in sets of Y-chromosome located probes but I extract these from an OrgDb. It would be helpful if you could post some code that shows where you get stuck. ...
written 7 days ago by
Guido Hooiveld • 2.5k
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... Hi,
With interest I have read this thread, because some of our transcriptome experiments have a complex design for which analysis by linear mixed models would be useful. However, considering the fact that the `lme4` and `variancePartition` results apparently don’t differ (actually, are in agreement) ...
written 8 days ago by
Guido Hooiveld • 2.5k
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Answer:
A: CDF not found
... The Affymetrix Clariom S Rat arrays are so-called 3rd generation expression arrays, and the analysis of these type of arrays is NOT possible anymore with the library `affy` (see e.g. [here][1]). In contrast, you should use the library `oligo` ([here][2]) + the corresponding PdInfo (platform design i ...
written 4 weeks ago by
Guido Hooiveld • 2.5k
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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 9 weeks 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 10 weeks 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 11 weeks ago by
Guido Hooiveld • 2.5k
• updated
11 weeks ago by
James W. MacDonald ♦ 51k
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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 12 weeks 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 12 weeks 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 3 months ago by
Guido Hooiveld • 2.5k
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