User: Guido Hooiveld
Guido Hooiveld • 2.4k
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Posts by Guido Hooiveld
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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 17 days ago by
Guido Hooiveld • 2.4k
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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 24 days ago by
Guido Hooiveld • 2.4k
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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 29 days ago by
Guido Hooiveld • 2.4k
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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 4 weeks ago by
Guido Hooiveld • 2.4k
• updated
4 weeks ago by
Martin Morgan ♦♦ 23k
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... I am not an expert on salmon, but a quick view on NCBI website shows that the number of annotated genes (that all have a gene symbol) indeed equals 57k (to be specific: 57,946 [incl. 6 discontinued genes]). This number is in line with what you reported... In other words, why do you expect 97k gene e ...
written 5 weeks ago by
Guido Hooiveld • 2.4k
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Answer:
A: error after normalizing data
... Hi,
Since you didn't post any code, we have to guess what you did, and what you would like to achieve.... However, based on the very brief error message I assume you are analyzing an HTA array data set.
I would suggest to have a look at this thread, in which some code is given that can get you start ...
written 9 weeks ago by
Guido Hooiveld • 2.4k
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Comment:
C: project miran packages
... The error you got:
All the CEL files must be of the same type.
is rather self-explanatory. It means that either a) you have an experiment consisting of some CEL files that you **think** are mirna 3.0 arrays, but rather are (all) of a different type; or b) that your CEL files are of 'mixed or ...
written 10 weeks ago by
Guido Hooiveld • 2.4k
0
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1
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Answer:
A: project miran packages
... Affymetrix (and hence Bioconductor) doesn't provide a chip definition file (CDF) for this type of array. To process your CEL files you will need the `oligo` package ([here][1]) and corresponding platform design package ([here][2]).
You may want to check e.g. this post of James McDonald ([here][3]) f ...
written 10 weeks ago by
Guido Hooiveld • 2.4k
3
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... As said in the related thread started by you, and that now is deleted (also by you?!), these are 3rd generation Affymetrix arrays for which NO Chip Definition File (CDF) is available. As a result, these arrays can NOT be analyzed using the library `affy`, but rather should be analyzed using `oligo` ...
written 11 weeks ago by
Guido Hooiveld • 2.4k
3
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1
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47
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... There are several issues regarding your question:
- you didn't post the full code you used to obtain object `data.raw`.
- `limma` as such doesn't have functionality to preprocess (normalize) Affymetrix arrays (CEL files); you will have to do this separately using functionality available in the libr ...
written 12 weeks ago by
Guido Hooiveld • 2.4k
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