User: Natasha

gravatar for Natasha
Natasha40
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21 hours ago
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2 years, 7 months ago
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Posts by Natasha

<prev • 127 results • page 1 of 13 • next >
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Mapping BRENDA ligand id to Kegg Compound id
... Hi All, I'd like to know if there is a way to map ligand id obtained from BRENDA to other ids like SABIO compound id/ KEGG compound id. Thanks ...
brenda ligand written 21 hours ago by Natasha40
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Comment: C: Question on performing RMA normalization
... @Kevin Blighe Thanks a lot for the response. I created a new post for this question [here][1]. [1]: https://www.biostars.org/p/403858/ ...
written 4 months ago by Natasha40
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Mapping probe ids in microarray data to gene ids
... I've performed RMA normalization of intensity data in raw files of dataset GSE1133. The output obtained after normalization is in the following format GSM18584.CEL GSM18585.CEL GSM18586.CEL GSM18587.CEL AFFX-18SRNAMur/X00686_3_at 10.324639 10.309749 7. ...
gene microarray written 4 months ago by Natasha40 • updated 4 months ago by mkgupta.bioinfo170
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Comment: C: Question on performing RMA normalization
... Hi, Thanks a lot. That was my mistake. I could run the code and perform normalization Background correcting Normalizing Calculating Expression GSM18584.CEL GSM18585.CEL GSM18586.CEL GSM18587.CEL AFFX-18SRNAMur/X00686_3_at 10.324639 10.309749 ...
written 4 months ago by Natasha40
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Comment: C: Question on performing RMA normalization
... Hi I tried to unzip using (sapply(paste("data", cels, sep = "/"), gunzip) and run the code again. Get the same error for some reason Error: the following are not valid files: GSM18584.CEL GSM18585.CEL GSM18586.CEL ...
written 4 months ago by Natasha40
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Question on performing RMA normalization
... I am following the tutorial given [here][1] to perform RMA normalization of dataset GSE1133 using the following code in R. cdf libraries of platform gpl1073 and gpl1074 have been installed following the description given [here][2] library(Biobase) library(GEOquery) library(affy) lib ...
rma microarray written 4 months ago by Natasha40
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Comment: C: Normalizing raw data from Affymetrix expression microarrays
... Thanks. Yes, I could find 3 platforms : GPL96, GPL1073 and GPL1074. I could also get the corresponding gsets by doing library(Biobase) library(GEOquery) library(limma) # load series and platform data from GEO gset <- getGEO("GSE1133", GSEMatrix =TRUE, AnnotGPL=TRUE ...
written 4 months ago by Natasha40
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Comment: C: Normalizing raw data from Affymetrix expression microarrays
... Many thanks for the response. I am using Bioconductor packages now. I would to confirm whether the following commands are correct for assigning the cdf file for normalization. On GEO, 3 platforms are given so I am a little confused. GEO : [GSE1133][1] biocLite("hgu133acdf") raw.data = Rea ...
written 4 months ago by Natasha40
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Normalizing raw data from Affymetrix expression microarrays
... Is there any python package that can be used for normalizing data from Affmetrix expression microarrays? I understand the Affy library of Bioconductor package in R can be used. However, I would like to perform normalization using libraries in python. I found [pyaffy][1] available on github. But th ...
rma gene-expression cel written 4 months ago by Natasha40 • updated 4 months ago by ATpoint30k
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Comment: C: Processing gene expression data
... Thank you. I am trying to normalize using the following code library(affy) %IN bioconductor package Data <- ReadAffy() % reads all .CEL files eset <- rma(Data) % RMA normalization Is this right? I am trying to normalize all samples(i.e GSM18584 to 18705) together ...
written 4 months ago by Natasha40

Latest awards to Natasha

Popular Question 4 months ago, created a question with more than 1,000 views. For Interpreting distance from clustal omega
Popular Question 4 months ago, created a question with more than 1,000 views. For Multiple probe for same gene
Supporter 5 months ago, voted at least 25 times.
Centurion 5 months ago, created 100 posts.
Popular Question 8 months ago, created a question with more than 1,000 views. For Identify Transcription factor from a list of genes
Popular Question 17 months ago, created a question with more than 1,000 views. For Identify Transcription factor from a list of genes
Popular Question 17 months ago, created a question with more than 1,000 views. For Interpreting distance from clustal omega

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