User: nkabo

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nkabo10
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Posts by nkabo

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Comment: C: How to find which genes are transciptional factors from a list of genes?
... Thank you for your reply, I am working on human as organism. Which database I could use to obtain transcription factors for human? ...
written 7 months ago by nkabo10
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How to find which genes are transcriptional factors from a list of genes?
... I have list of genes and I would like to have protein-coding and transcription factor genes from that list. Is there a database or tool which I can put my list of genes as an input and get the transcription factors ones only as an output? Thanks! ...
gene transcription factor written 7 months ago by nkabo10 • updated 7 months ago by RamRS25k
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Comment: C: How to subset ExpressionSet based on vector of sample names
... Thank you for your reply, it works but it gives a matrix I should have an ExpressionSet. ...
written 8 months ago by nkabo10
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Comment: C: How to subset ExpressionSet based on vector of sample names
... Thank you for your reply, I checked it again and it works fine but it gives an expression matrix, I would like to have it as ExpressionSet. ...
written 8 months ago by nkabo10
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How to subset ExpressionSet based on vector of sample names
... I have an ExpressionSet object composed of 37 samples for HCC and cirrhosis situation and I would like to subset it according to names that I specified in two vectors. As a result, I want to have 2 expression arrays (one set is for HCC and other is for cirrhosis) after I subset this ExpressionSet. I ...
R bioconductor expressionset subset written 8 months ago by nkabo10
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Comment: C: How to process gene expression data from Affymetrix U133 Plus 2.0 in Python
... Thank you for the reply. I had used the workflow and I expected to have approximately 26k data points but it ended up with over 48k probes. Is it expected or did I do something wrong during processing? ...
written 8 months ago by nkabo10
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How to process gene expression data from Affymetrix U133 Plus 2.0 in Python
... Hello, I have a gene expression dataset taken from ArrayExpress based on Affymetrix U133 Plus 2.0. Is there a workflow that describes how to complete the steps below: 1) Replacing probe IDs with gene names, 2) Removing the probes which are not specific to only one gene 3) Getting the mean of ex ...
python affymetrix gene expression data human written 9 months ago by nkabo10
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How to find average expression value for genes with multiple probes -Affymetrix
... Hi, I have expression data from the Affymetrix GeneChip Human Genome U133 Plus 2.0 array, it is consisted of expression values for 54715 probes for each individual. I have a XLS file that matches probe IDs to its corresponding gene name. There are some genes associated with multiple probes. In ord ...
expression data microarray affymetrix written 10 months ago by nkabo10 • updated 10 months ago by ATpoint29k
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Comment: C: How to convert .cel to .fastq for miRNA analysis?
... So do I need another pipeline to analyze .cel file and make it a "sequence" file? ...
written 16 months ago by nkabo10
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How to convert .cel to .fastq for miRNA analysis?
... I would like to do miRNA analysis for a dataset that I have found via an article. The pipeline I have in order to analyze the miR data requires the data file to be a .fastq file. However, the dataset I received is composed of .cel files. Is it possible to convert .cel datafiles to .fastq? Thanks ...
next-gen rna sequencing mirna analysis written 16 months ago by nkabo10

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Supporter 8 months ago, voted at least 25 times.
Popular Question 14 months ago, created a question with more than 1,000 views. For Tool for calculating variant frequency
Great Question 3.5 years ago, created a question with more than 5,000 views. For Finding number of duplicates in R
Epic Question 3.5 years ago, created a question with more than 10,000 views. For Finding number of duplicates in R
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Calculating variant frequency in R
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Tool for calculating variant frequency
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Finding number of duplicates in R

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