User: Guido Hooiveld
Guido Hooiveld • 2.2k
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- Wageningen University, Wageningen, the Netherlands
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Posts by Guido Hooiveld
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... In order to calculate the MAS5-like detection calls (P, A, M), you will need the MM probes. Since you meanwhile know that these are lacking on this PM only array, how could you do this....?
Answer: you can't, so what you would like to do makes no sense....
The only alternative I know of that allows ...
written 27 days ago by
Guido Hooiveld • 2.2k
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... P-values of what? I assume you would like to compare two or more groups? Use the package limma for this (link), and 'feed' it the normalized data. Please be sure to carefully read the very extensive vignette (manual), since this document contains tons of examples/approaches on how to do this.
Also, ...
written 27 days ago by
Guido Hooiveld • 2.2k
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... What exactly is "RMA-Alt-splicing Normalisation"? Has it to do with the (non-Bioconductor) software 'AltAnalyze'? In any case, I am not familiar with both, but a quick glance at 'AltAnalyze' suggested to me that it makes use of Affymetrix Power Tools (APT), which uses the files than can be downloade ...
written 28 days ago by
Guido Hooiveld • 2.2k
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... Mmm, did I not basically answer your question in this thread? Here
Also, if you did some searching on (for example) this forum you would have learned that for the newest generation of Affymetrix arrays CDF files are not anymore provided (and used). see e.g. here. The packages oligo or xps are the w ...
written 28 days ago by
Guido Hooiveld • 2.2k
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... Please familiarize yourselves a little with the design of the Affymetrix arrays. The design of the HG-U133+ PM array differs from the 'original' HG-U133 Plus 2.0 array at two points, of which this is the relevant one: "Only perfect match (PM) probes from the cartridge design were retained, while mi ...
written 28 days ago by
Guido Hooiveld • 2.2k
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... Unfortunately biocLite() will not automagically download the custom (remapped) CDF you would like to use from the repository of the MBNI group. You rather have to download them directly by:
install.packages("http://mbni.org/customcdf/22.0.0/entrezg.download/hgu133ahsentrezgcdf_22.0.0.tar.gz", type ...
written 29 days ago by
Guido Hooiveld • 2.2k
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... No, you should not use / generate a CDF to analyze these arrays.
You rather should analyze these type of arrays using the package oligo (link) in combination with the corresponding platform design package (link). In the vignette (PDF) of oligo it is explained how to create the plots you are interes ...
written 4 weeks ago by
Guido Hooiveld • 2.2k
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... Likely because Guangchuang did not specify any significance cutoff (he set the cutoffs for both p-value and q-value to 1, i.e. no significance filtering), and you set the p-value cutoff at 0.05 (which is apparently too strict for your experiment).
...
written 5 weeks ago by
Guido Hooiveld • 2.2k
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... Basically the message tells you what is going on: for the current version of Bioconductor (R-3.4.x) only 3 predefined frozen RMA vectors are available for mouse arrays, i.e. mogene.1.0.st.v1frmavecs, mouse4302frmavecs, and mouse430a2frmavecs. For the arrays you mention these vectors/info isn't avail ...
written 6 weeks ago by
Guido Hooiveld • 2.2k
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... Aha, AFAIK in that case you can use the argument species.KEGG = "ko" when using the function kegga().
Assuming DEGs is a character vector with the differentially expressed KO IDs, something like:
k<- kegga(DEGs, species.KEGG = "ko", FDR = 0.05)
...
written 8 weeks ago by
Guido Hooiveld • 2.2k
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