User: Amy Mikhail

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Amy Mikhail460
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Posts by Amy Mikhail

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"AveExp" column has dissappeared from limma topTable
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written 12.6 years ago by Amy Mikhail460
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Signal above negative controls in a two-color experiment - limma?
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written 12.7 years ago by Amy Mikhail460
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written 12.7 years ago by Amy Mikhail460
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[Bioc] Removing outlier/masked probes and gcRMA
... Hi Andrew, Just thought I'd refer you to a discussion on the list a few weeks ago about removal of probesets, which might help. As I understand it, the problem is that you need to remove your probes (or probesets) from the cdf as well as your affybatch object, so that they match. There is a chu ...
cdf affy gcrma written 12.8 years ago by Amy Mikhail460
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Comment: C: Some Genefilter questions
... Hi Jenny, Robert, Thanks a million, it has worked ... now I can have a look and see if removing the probesets actually made a difference :) - will let you know... Cheers, Amy > Oops - forgot to mention in my last post that the only way I've been able > to remove probesets from AffyBatch obj ...
written 12.9 years ago by Amy Mikhail460
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Comment: C: Some Genefilter questions
... Hi Jenny, Thanks - just realised my mistake; I forgot that I was just trying to create the character vector and the next bit was already in your code... Cheers, Amy ---------------------------------------------------------------------- ----- Amy > Oops - forgot to mention in my last post that ...
written 12.9 years ago by Amy Mikhail460
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Answer: A: Some Genefilter questions
... Hi all, Sorry to bring this interesting discussion back to the mundane again for a minute, but when trying to create the "parasites" character vector from my affybatch object, removing the parasite probe sets with Robert's suggested code is giving me an error: > parasites <- grep("^Pf", gen ...
written 12.9 years ago by Amy Mikhail460
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Comment: C: Some Genefilter questions
... Hi all, Jenny, just wanted to clarify what you said; you reckon if I only want to remove the foreign species probesets I should do this before preprocessing, but if I want to remove e.g. absent calls from my own species probes I should do this after preprocessing. Is this right? Also, how do I cr ...
written 13.0 years ago by Amy Mikhail460
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Comment: C: Some Genefilter questions
... Hi all, I am curious to see how they compare too - as soon as I have the subsetting and character vector sorted I will try both and let you know how it turns out. Out of interest - would it also be possible to carry out the background correction on the full dataset, then remove the parasite probe ...
written 13.0 years ago by Amy Mikhail460
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Comment: C: Some Genefilter questions
... Hi Robert and Jim, Many thanks for your advice. I have some more questions... First, I tried what Robert suggested on my expression set. However I got a strange result: > load("E:\\Amy - Bioconductor analysis\\03. Base age\\Affymetrix - Base Age results & analysis\\Baseage - RMA normalis ...
written 13.0 years ago by Amy Mikhail460

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Popular Question 11.1 years ago, created a question with more than 1,000 views. For read.GenePix not opening connection

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