User: asalimih

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asalimih20
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2 years, 4 months ago
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In the way of learning Bioinformatics.

Posts by asalimih

<prev • 21 results • page 1 of 3 • next >
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Comment: C: GSEA preranking metric for RNA Seq
... what would be your answer if the question was about the GSEA program of Broad Institute? ...
written 4 months ago by asalimih20
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Answer: A: Microarray: How To Select One Of Multiple Probes Corresponding To A Gene
... Although this question is old but i found this answer from one of reddit bioinformatics forum very useful. [link][1] [1]: https://www.reddit.com/r/bioinformatics/comments/544zqi/multiple_probes_for_one_gene/d7zpcxj?utm_source=share&utm_medium=web2x ...
written 10 months ago by asalimih20
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Comment: C: frma normalization function not working on ExpressionFeatureSet object
... yes i could reproduce the error : Beginning Median SE Calculation ... Error in if (any(w < 0)) { : missing value where TRUE/FALSE needed ...
written 10 months ago by asalimih20
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Comment: C: frma normalization function not working on ExpressionFeatureSet object
... Thank you for your time and help. Here is the package maintainer's reply: > Unfortunately, I never created the vectors for the hgu133b platform. > You could create your own using the frmaTools package, but that's > fairly involved. for now I'll just use rma. but I'll try frmaTools in fut ...
written 10 months ago by asalimih20
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Comment: C: frma normalization function not working on ExpressionFeatureSet object
... Thank you very much. yes it works but there is another problem. if you try your code on `A-AFFY-34` you'll face an error saying `hgu133bfrmavecs` package is required. and actually we have no package named `hgu133bfrmavecs` . ...
written 10 months ago by asalimih20
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Comment: C: frma normalization function not working on ExpressionFeatureSet object
... I edited my post and added my code. ...
written 10 months ago by asalimih20
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frma normalization function not working on ExpressionFeatureSet object
... Hello, I have an ExpressionFeatureSet object which is created by ae2bioc function from ArrayExpress package. Now i want to perform a Frozen Robust Multiarray Analysis using frma function from frma package but i get this error: object must be of class AffyBatch, ExonFeatureSet, or GeneFeatur ...
normalization rma frma microarray preprocess written 10 months ago by asalimih20 • updated 10 months ago by Kevin Blighe61k
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Comment: C: Integration of Microarray datasets with different platforms and biological group
... Can I consider these platforms as the same: Affymetrix Human Genome U133A+U133B and Affymetrix Human Genome U133 plus? ...
written 10 months ago by asalimih20
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Comment: C: Integration of Microarray datasets with different platforms and biological group
... if platforms were the same would this analysis be possible to perform? (based on groups i mentioned) ...
written 10 months ago by asalimih20
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Comment: C: Integration of Microarray datasets with different platforms and biological group
... Thanks for your reply. another question, for example i want to check for a Gene if there is a significant upregulation from TypeB to TypeE. i perform DEA on GSE1 for TypeB vs TypeA and a separate DEA on GSE2 for TypeA vs TypeE. now if there was an upregulation from TypeB to TypeA and an upregulation ...
written 10 months ago by asalimih20

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