User: Joao Sollari Lopes

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Posts by Joao Sollari Lopes

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Mapping Affymetrix annotations with Bioconductor annotations
... Hi Jim, Following on the discussion on annotation in Affymetrix Gene ST arrays, I wonder if there is a standard way to deal with multiple mRNAs (from different genes) that are assigned to the same transcript cluster. Is it generally accepted to follow the naive approach of picking the first mrna of ...
annotation organism zebrafish cdf affy annotationforge written 5.7 years ago by Joao Sollari Lopes80 • updated 5.7 years ago by James W. MacDonald50k
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affymtrix transcript_cluster categories
... Hi, I am using Zebrafish Gene 1.1 ST Array Strip from Affymetrix. Affymetrix categorizes the transcript clusters as: main - part of the main design control->affx - a standard AFFX control control->chip - a chip control control->bgp->antigenomic - contains antigenomic background probes ...
normalization zebrafish written 5.8 years ago by Joao Sollari Lopes80 • updated 5.8 years ago by James W. MacDonald50k
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Comment: C: blast probe clusters when using Affymetrix Gene Array Strips
... Hi Jim, Thanks for your help once again! Joao On 09/04/2013 03:08 PM, James W. MacDonald wrote: > Hi Joao, > > On Wednesday, September 04, 2013 6:11:12 AM, Joao Sollari Lopes wrote: >> Hi, >> >> I am using Zebrafish Gene 1.1 ST Array Strip, I have found some >> tra ...
written 5.8 years ago by Joao Sollari Lopes80
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blast probe clusters when using Affymetrix Gene Array Strips
... Hi, I am using Zebrafish Gene 1.1 ST Array Strip, I have found some transcript clusters that are differentially expressed but are not annotated (although they belong to the "main" design of the array). I would like to blast them, but I am not sure what to blast as each transcript cluster has variou ...
zebrafish written 5.8 years ago by Joao Sollari Lopes80 • updated 5.8 years ago by James W. MacDonald50k
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accessing NetAffx annotation with "oligo" package
... Hi, I am using "oligo" and I have attached NetAffx annotation using getNetAffx(). Are there any ready-to-use functions to access the attached NetAffx annotation in the ExpressionSet object? Thank you very much, Joao Lopes Instituto Gulbenkian de Ciencia ...
annotation written 5.8 years ago by Joao Sollari Lopes80
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Comment: C: Mapping Affymetrix annotations with Bioconductor annotations
... Hi Jim, Many thanks for that! All the best, Joao On 08/29/2013 04:22 PM, James W. MacDonald wrote: > Hi Joao, > > Unfortunately there are no readily available packages for annotating > all the new model organism arrays from Affy. However, the functions to > create your own annotati ...
written 5.8 years ago by Joao Sollari Lopes80
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Comment: C: Mapping Affymetrix annotations with Bioconductor annotations
... Hi Jim, Thanks for your quick reply. Actually I was able to do some kind of mapping through the position of the probes in the strips using the files: zebgene11stdrentrezgprobe_17.1.0.tar.gz (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/17 .1.0/entrezg.download/zebgene11stdren ...
written 5.8 years ago by Joao Sollari Lopes80
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Mapping Affymetrix annotations with Bioconductor annotations
... Hi, I am trying to compare the annotations provided by Affymetrix with the ones provided by Bioconductor for Zebrafish Gene 1.1 ST Array Strip I have compared the files zebgene11stdrentrezg.db_17.1.0.tar.gz (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/17 .1.0/entrezg.downl ...
written 5.8 years ago by Joao Sollari Lopes80 • updated 5.8 years ago by James W. MacDonald50k

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Popular Question 5.7 years ago, created a question with more than 1,000 views. For Mapping Affymetrix annotations with Bioconductor annotations

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