User: Natasha

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Natasha40
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8 months ago
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3 years, 7 months ago
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Posts by Natasha

<prev • 129 results • page 2 of 13 • next >
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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 16 months ago by Natasha40 • updated 16 months ago by ATpoint46k
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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 16 months ago by Natasha40
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Comment: C: Processing gene expression data
... Thank you. It is mentioned that GPL1073 GNF1M platform is for Mouse (GSM18584 to 18705) GPL1074 GNF1H is for Human. (18706 to 18863) However, I couldn't find the platform id in the CEL files . ...
written 16 months ago by Natasha40
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Comment: C: Processing gene expression data
... Many thanks for the response. Yes, the raw CEL files are available [here][1]. The figure 1 that I want to reproduce is available in this article. (Please find the link [here][2]) . Description of how the figure was created can be found in the supplementary. Also, figure one has been created using ...
written 16 months ago by Natasha40
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Processing gene expression data
... This is a follow up to my [previous question][1]. I would like to implement the following steps given in the supplementary file of [this study][2] to reproduce the figure 1 displayed in the paper. > We used Affymetrix microarray data from a recent thorough analysis of > the mouse and human ...
gene-expression written 16 months ago by Natasha40 • updated 16 months ago by c.chakraborty160
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Comment: C: Clustering tissues using gene expression data
... @ATpoint Apparently, symatlas has been navigated to BioGPS and the supplementary files are available [here][1]. I could find the same files on GEO with accession number [GSE1133][2]. However , the data is available in different formats like CDF, CIF, GIN, PSI, SIF, PROBE, TAB, TXT. I am not sure wh ...
written 16 months ago by Natasha40
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Comment: C: Clustering tissues using gene expression data
... Thanks a lot for the response. In the section on 'Microarray procedure' of the reference , "A gene atlas of the mouse and human protein-encoding transcriptomes" it is mentioned that the raw files can be found in http://symatlas.gnf.org. However, I couldn't locate the raw files. ...
written 16 months ago by Natasha40
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Comment: C: Clustering tissues using gene expression data
... Yes I wrote an email to [Prof. Bork][1] who is the corresponding author. Unfortunately, I didn't get any response yet. [1]: http://www.bork.embl.de/j/ ...
written 16 months ago by Natasha40
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Clustering tissues using gene expression data
... I would like reproduce the tissue cluster tree reported in figure 1 and figure 2 of this [paper][1] In the supplementary document related with this paper, it is mentioned that the raw intensity data from "A gene atlas of the mouse and human protein-encoding transcriptomes" has been used. However, ...
gene-expression clustering written 16 months ago by Natasha40 • updated 13 months ago by Biostar ♦♦ 20
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Comment: C: Isoforms of an enzyme
... Thanks a lot . I could find all the data in the enzyme.dat file provided [here][1]. I've to parse the isoform information from the dat file. I'd like to know if there are scripts that are available to parse this file. [1]: ftp://ftp.expasy.org/databases/enzyme ...
written 17 months ago by Natasha40

Latest awards to Natasha

Popular Question 8 months ago, created a question with more than 1,000 views. For Transcription factor of a gene (Humans)
Popular Question 10 months ago, created a question with more than 1,000 views. For Parsing values from GSE file
Popular Question 11 months ago, created a question with more than 1,000 views. For Interpreting distance from clustal omega
Popular Question 16 months ago, created a question with more than 1,000 views. For Interpreting distance from clustal omega
Popular Question 16 months ago, created a question with more than 1,000 views. For Multiple probe for same gene
Supporter 17 months ago, voted at least 25 times.
Centurion 18 months ago, created 100 posts.
Popular Question 20 months ago, created a question with more than 1,000 views. For Identify Transcription factor from a list of genes
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Identify Transcription factor from a list of genes
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Interpreting distance from clustal omega

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