User: Guido Hooiveld
Guido Hooiveld • 2.3k
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Posts by Guido Hooiveld
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Comment:
C: Pathview results interpretation
... It would have been helpful if you also posted your code and/or graph, because now we have to *assume* the things you did... Anyway, if I plot/overlay my gene expression data using pathview, rectangles correspond indeed to genes/enzymes. If you plot fold changes, red is 'increased', and green is 'dec ...
written 6 weeks ago by
Guido Hooiveld • 2.3k
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Comment:
C: Affe package mas5 error
... It's working fine for me using some similar old (1st generation) mouse arrays that I had at hand.
However, I noticed that you are using version 18 of the custom CDF, which was released more than 4 years ago.... Maybe these old CDFs are not compatible anymore with the current version of R/BioC? The ...
written 6 weeks ago by
Guido Hooiveld • 2.3k
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... Thanks you both for your valuable answers!
@ Ryan: method="nestedF" indeed gives the same number of genes.
@ Gordon: yes, point taken! I was so caught up with details that I could not see the wood for the trees...
...
written 10 weeks ago by
Guido Hooiveld • 2.3k
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... I am a bit confused on how to perform and/or interpret the results of an ANOVA-like analysis in limma. I would like to compare 3 pairwise contrasts, essentially as described in paragraph 9.3 of the limma users guide. My code is running fine, and the output of the eBayes function nicely returns the ( ...
written 10 weeks ago by
Guido Hooiveld • 2.3k
• updated 10 weeks ago by
Gordon Smyth ♦ 34k
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... In the past I also struggled a bit with this... See the thread on how I got it working here.
Could it be you are calling the install.packages() function without being in the proper directory, and as a result the created OrgDb files cannot be found and installed?
I usually 'set' the working director ...
written 10 weeks ago by
Guido Hooiveld • 2.3k
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... From the vignette here:
In clusterProfiler, groupGO is designed for gene classification based on GO distribution at a specific level.
Over-representation test were implemented in clusterProfiler. For calculation details and explanation of parameters, please refer to the vignette of DOSE. enrichGO ...
written 10 weeks ago by
Guido Hooiveld • 2.3k
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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 3 months ago by
Guido Hooiveld • 2.3k
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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 3 months ago by
Guido Hooiveld • 2.3k
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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 3 months ago by
Guido Hooiveld • 2.3k
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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 3 months ago by
Guido Hooiveld • 2.3k
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