User: Kamila Naxerova

gravatar for Kamila Naxerova
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6 years, 7 months ago
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Posts by Kamila Naxerova

<prev • 10 results • page 1 of 1 • next >
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fRMA for Gene ST arrays
... Dear list, to preprocess Affymetrix whole transcript arrays, use of oligo and xps is recommended over the affy package. I am interested in using the GNUSE algorithm to assign quality scores to some arrays, and would also like to try out the barcode function in the frma package. I am now wondering.. ...
affy oligo frma assign written 6.6 years ago by Kamila Naxerova100 • updated 6.6 years ago by Matthew McCall830
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Answer: A: Proper use of annotation package
... Thanks for your prompt reply Jim! Actually I am afraid there is some deeper lack of knowledge on my part here... Some of the ids that topTable() returns simply don't exist in the annotation package, period. They also don't exist when I search for them in the NetAffx Analysis center. What are these ...
written 6.7 years ago by Kamila Naxerova100
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Proper use of annotation package
... Hi all, I have a little problem using an annotation package that I know how to work around, but I am wondering how to do it more elegantly and efficiently. I am analyzing a bunch of Mouse Gene 2.0 ST arrays. I built my own annotation package (with much help from all of you!). I am using Limma and ...
annotation probe written 6.7 years ago by Kamila Naxerova100
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Comment: C: Analysis of Affymetrix Mouse Gene 2.0 ST arrays
... Haha, I don't mind rubbing against that belly. It's like playing a game... tyring to figure out how to get to the 40th level to face the "final enemy". Your strategy worked, thank you! I am including all code up to RMA normalization (yay! I am there!) below, perhaps it will save somebody a few hour ...
written 6.7 years ago by Kamila Naxerova100
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Comment: C: Analysis of Affymetrix Mouse Gene 2.0 ST arrays
... Thanks Jim. Of course the annotation package does not contain probe --> probe set information. What was I thinking?!?? What I had not realized was that I needed to build the pd.mogene.2.0.st package myself first, because it also does not exist on Bioconductor. So I just downloaded all the requir ...
written 6.7 years ago by Kamila Naxerova100
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Comment: C: Analysis of Affymetrix Mouse Gene 2.0 ST arrays
... Dear all, I am afraid I have to ask for help with the Mouse Gene 2.0 ST annotation package one more time. It looked like I created it successfully, but when I try to use it to read in cel files with the oligo package, I get a cryptic error message. Any suggestions would be much appreciated! > a ...
written 6.7 years ago by Kamila Naxerova100
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Comment: C: Analysis of Affymetrix Mouse Gene 2.0 ST arrays
... Dear Christian and Jim, many thanks to both of you for your explanations. Your hard work paid off, and I have finally understood everything and managed to build my annotation package!!!! I wrote a little script similar to what Jim was suggesting, namely picking the first RefSeq- like thing I came ...
written 6.7 years ago by Kamila Naxerova100
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Comment: C: Analysis of Affymetrix Mouse Gene 2.0 ST arrays
... Hi Jim, thank you for your helpful reply. I have a few follow-up questions. > > I should throw in my obligatory cautionary statement about summarizing > Gene ST data at the probeset (as compared to the transcript) level. If > you look at the number of probes/probeset, there are a huge n ...
written 6.7 years ago by Kamila Naxerova100
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Analysis of Affymetrix Mouse Gene 2.0 ST arrays
... Dear all, I am analyzing a set of Affymetrix Mouse Gene 2.0 ST arrays. I am quite familiar with 3'-biased chips, but this is my first time looking at data from WT arrays. I have a few general questions -- any advice would be appreciated to speed up my learning process. 1) I have already read on th ...
annotation normalization go process oligo written 6.7 years ago by Kamila Naxerova100 • updated 6.7 years ago by James W. MacDonald51k
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Affymetrix miRNA array normalization
... Dear list, I was searching the archives for discussions about the Affymetrix miRNA chip... there are only a few threads and most of them are almost a year old. I was wondering whether in the meantime people had gathered some experience with analysis strategies - normalization in particular - and w ...
mirna normalization written 9.4 years ago by Kamila Naxerova100 • updated 9.4 years ago by Thomas Hampton20

Latest awards to Kamila Naxerova

Great Question 6.6 years ago, created a question with more than 5,000 views. For Analysis of Affymetrix Mouse Gene 2.0 ST arrays
Popular Question 6.6 years ago, created a question with more than 1,000 views. For Analysis of Affymetrix Mouse Gene 2.0 ST arrays

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