User: priya.bmg

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priya.bmg0
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Posts by priya.bmg

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Comment: C: Access metadata in GEO expression datasets
... Yes there is not enough memory to load the data using the getGEO command. Is there a way around to save the data and do the analysis without much memory usage? ...
written 6 days ago by priya.bmg0
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Comment: A: Access metadata in GEO expression datasets
... gds <- getGEO("GSE25219") **Got the below error message:** Found 2 file(s) GSE25219-GPL5175_series_matrix.txt.gz Using locally cached version: C:\Users\dell\AppData\Local\Temp\RtmpGGb51t/GSE25219-GPL5175_series_matrix.txt.gz Error in read_lines_(ds, skip_empty_row ...
written 6 days ago by priya.bmg0 • updated 6 days ago by genomax91k
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Access metadata in GEO expression datasets
... Hi, I have been trying to analyze expression datasets from NCBI GEO database. Because of memory allocation problem, I am not able to load the expression text file in R. But I could save the SOFT file in temporary file location. Is there a way to access few rows and columns in this SOFT file? I trie ...
geo R gene expression written 7 days ago by priya.bmg0
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Comment: C: Time steps in node perturbation analysis
... Thanks. The question is "how perturbation (knock-out) of gene A affects a gene B expression". I will show the shape of the curve to show how the system evolves in response to the perturbation from time step t = 0 and t =150. I have been thinking and yes you are right average expression doesn't seem ...
written 7 days ago by priya.bmg0
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Comment: C: Time steps in node perturbation analysis
... @Joe Thanks. It is not a homework question. Sorry if it sounded that way. I have always been reporting the regulation of gene expression at the last time step (ts =150). Now, it struck to me then about the previous time steps. Should I take an average of the regulation of gene expression at all the ...
written 8 days ago by priya.bmg0
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Time steps in node perturbation analysis
... Hi, Why do we specify time steps while performing simulations?. For example, in node perturbation analysis, I perturb Gene A (knock-out) and simulate how this perturbation affects expression of other genes. I do this perturbation for time steps ts=0 to ts=150. How is the result at ts=0 different fr ...
simulations expression perturbation time steps written 9 days ago by priya.bmg0 • updated 9 days ago by Joe18k
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Comment: C: Genes inhibiting each other's expression
... Thank you for the explanation ...
written 23 days ago by priya.bmg0
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Forum: Genes inhibiting each other's expression
... Hi, Can two genes repress each other's expression?. For example, Gene A inhibits Gene B, Gene B inhibits Gene A. Gene A is a transcription factor goes and binds to the promoter of Gene B and inhibits Gene B expression. Similarly, gene B is a transcription factor, inhibits Gene A expression. So, bot ...
forum gene expression written 4 weeks ago by priya.bmg0 • updated 4 weeks ago by i.sudbery9.4k
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Allelic variation in a population
... How to know if my gene is conserved in terms of allelic variation in a population? Should I look at the global minor allele frequency to know if the variation in a gene is conserved or not? Thanks Priya ...
conserved allelic variation written 22 months ago by priya.bmg0 • updated 22 months ago by genomax91k
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miRNA nomenclature for mature miRNA sequence
... Hi, Is both miR-9 and miR-9-5p are same? Can I consider miR-9-5p as miR-9? As some of the database, give a list of miRNAs, where for some of the miRNA, they also indicate either the long arm or short arm of the chromosome and for some of the miRNA, nothing is mentioned about the arm of chromosome. ...
rna-seq written 2.2 years ago by priya.bmg0 • updated 2.2 years ago by WouterDeCoster44k

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