User: teabonng

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teabonng30
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Posts by teabonng

<prev • 30 results • page 1 of 3 • next >
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Regression trees against background
... Hi Everyone, Do you know if there is an algorithm for implementing regression trees (random forest) while taking into account a background/control data? Much like Leo Breiman's unsupervised random forest but for regression? There the null background is a permuted matrix generated from the original ...
machine learning regression written 4 days ago by teabonng30
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GCRMA normalization from data frame
... Hi Everyone, I am analyzing multiple datasets from GEO, and I got the raw values. I need to perform GCRMA normalization, but this has to be from an AffyBatch object. Is there a way to directly perform gcrma or rma normalization directly on the data frame or matrix that I downloaded from GEO? Many ...
normalization microarray written 9 days ago by teabonng30
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Comment: C: Connectivity Map dataset
... Hi ATpoint, I have edited the question. Basically, i cannot download the raw .cel files of the rankMatrix.txt, a connection cannot be established. I have tried multiple ways of downloading but still nothing works. The problem seems to be on their server side. Thanks ...
written 5 months ago by teabonng30
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Construction of coexpression networks from multiple datasets
... Hi Everyone, I plan to construct coexpression networks to find modules using various independent datasets from databases such as GEO. Would it be valid that for each dataset, I calculate the fold changes of all genes with respect to untreated samples. Then I combine all the multiple datasets to cal ...
coexpression networks coexpression written 10 months ago by teabonng30
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Node degree-weighted graph
... Hi everyone, I would like to ask for suggestions as how to convert a weighted graph from an unweighted graph, with the weights based on the degrees of nodes in the edges. Also, if there is a good python package for this that can handle thousands of nodes. Thank you very much! ...
network biology written 11 months ago by teabonng30
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ChIP-Seq tag counts
... Hi Everyone, Can I use tag counts from ChIP-Seq data as inputs for machine learning? I did not call peaks, however, so that the features will not be simply binary. Thank you for your help. teabonng ...
chip-seq machine learning written 16 months ago by teabonng30 • updated 16 months ago by WouterDeCoster44k
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Histone modification patterns
... Hi Everyone, Can anyone refer me to a good reference that shows evidence that genes that belong to the same regulatory pathway have similar histone modification patterns that can be statistically analyzed? Thank you. ...
chromatin pattern written 18 months ago by teabonng30
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PPI networks in disease vs. healthy
... Hi Everyone, I was reading about some PPIs recently. Please excuse if my question is too simple. My question is, if i reconstruct PPIs from healthy and diseased individuals from omics data, would you expect that the reconstructed PPIs will be different, even if only a few nodes? ...
ppi networks written 18 months ago by teabonng30 • updated 18 months ago by Kevin Blighe61k
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Comment: C: Machine learning predictor has no correlation with output variable
... Hi Jean-Karim, Thank you for your help. I would just like to further clarify, since the logistic regression takes into account the individual contributions of each feature, but I did not add any interaction terms. In this case, I'm not sure if i can say that there is some interaction among the fea ...
written 19 months ago by teabonng30
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Machine learning predictor has no correlation with output variable
... Hi Everyone, I built a logistic regression classifier for predicting genes that has around 75% accuracy. Predictor A is a transcription factor that is a top predictor. However, when I look at the the scatterplot there is absolutely no correlation and the positive and negative examples show the same ...
machine learning written 19 months ago by teabonng30 • updated 19 months ago by Jean-Karim Heriche22k

Latest awards to teabonng

Popular Question 10 months ago, created a question with more than 1,000 views. For edgeR - normalized counts from multiple datasets
Popular Question 15 months ago, created a question with more than 1,000 views. For edger model matrix design of linear model

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