User: Natasha

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Natasha40
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6 months, 3 weeks ago
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3 years, 6 months ago
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Posts by Natasha

<prev • 129 results • page 1 of 13 • next >
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Comment: C: Create a tree with ontogenetic relationships between mammalian tissues
... Any suggestions will be highly appreciated ...
written 7 months ago by Natasha40
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Create a tree with ontogenetic relationships between mammalian tissues
... I have come across a study that shows ontogenetic relationships between mammalian tissues. Ref : [Similar Gene Expression Profiles Do Not Imply Similar Tissue Functions][1] I would like to ask for suggestions on how to create the tree that is shown in figure 2 of the above-mentioned paper. [1] ...
gene rna-seq written 7 months ago by Natasha40
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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 10 months 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 15 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 15 months ago by Natasha40 • updated 15 months ago by Manoj180
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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 15 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 15 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 15 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 15 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 15 months ago by Natasha40

Latest awards to Natasha

Popular Question 7 months ago, created a question with more than 1,000 views. For Transcription factor of a gene (Humans)
Popular Question 9 months ago, created a question with more than 1,000 views. For Parsing values from GSE file
Popular Question 10 months ago, created a question with more than 1,000 views. For Interpreting distance from clustal omega
Popular Question 15 months ago, created a question with more than 1,000 views. For Interpreting distance from clustal omega
Popular Question 15 months ago, created a question with more than 1,000 views. For Multiple probe for same gene
Supporter 16 months ago, voted at least 25 times.
Centurion 16 months ago, created 100 posts.
Popular Question 19 months ago, created a question with more than 1,000 views. For Identify Transcription factor from a list of genes
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Identify Transcription factor from a list of genes
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Interpreting distance from clustal omega

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