User: Natasha
Natasha • 40
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... 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 ...
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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
Natasha • 40
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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
Natasha • 40
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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
Natasha • 40
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... 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 ...
written 16 months ago by
Natasha • 40
• updated
16 months ago by
c.chakraborty • 160
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... @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
Natasha • 40
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... 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
Natasha • 40
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... 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
Natasha • 40
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... 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, ...
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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
Natasha • 40
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