User: Natasha

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Natasha30
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Posts by Natasha

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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 9 minutes ago by Natasha30
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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 1 day ago by Natasha30 • updated 1 hour ago by ATpoint24k
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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 1 day ago by Natasha30
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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 1 day ago by Natasha30
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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 1 day ago by Natasha30
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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 1 day ago by Natasha30 • updated 1 day ago by c.chakraborty150
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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 3 days ago by Natasha30
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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 3 days ago by Natasha30
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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 4 days ago by Natasha30
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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 5 days ago by Natasha30

Latest awards to Natasha

Supporter 4 weeks ago, voted at least 25 times.
Centurion 5 weeks ago, created 100 posts.
Popular Question 3 months ago, created a question with more than 1,000 views. For Identify Transcription factor from a list of genes
Popular Question 13 months ago, created a question with more than 1,000 views. For Identify Transcription factor from a list of genes
Popular Question 13 months ago, created a question with more than 1,000 views. For Interpreting distance from clustal omega

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