User: teabonng

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teabonng10
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Posts by teabonng

<prev • 15 results • page 1 of 2 • next >
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ChIP-Seq Read Counts
... Hi Everyone, I am very new to ChIP-Seq analysis, but i will be analyzing data from multiple studies. However, some ChIP seq studies do not have Input to compare the distribution of mapped reads, so I cannot do peak calling. In this case, is it common practice to simply get the normalized counts (li ...
chip-seq written 9 days ago by teabonng10
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Comment: C: Sam to bowtie native format
... Thank you so much for this. ...
written 9 days ago by teabonng10
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Comment: C: Sam to bowtie native format
... Thanks for the replies, now I understand. ...
written 9 days ago by teabonng10
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Sam to bowtie native format
... Hi everyone, Does anyone know how to convert .sam files to the native bowtie format? I need this for peak calling using QuEST software for ChIP seq data. Thanks a bunch! teabonng ...
quest chip-seq written 12 days ago by teabonng10 • updated 12 days ago by h.mon18k
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Comment: C: Hierarchical clustering evaluation
... The output of the dynamictree cut package in R is more than 90 clusters. I am clustering more than 10,000 genes based on their gene expression across various treatments. I cannot check if the genes in the same cluster are different because that is my objective, to learn which genes behave the same ...
written 5 weeks ago by teabonng10
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Hierarchical clustering evaluation
... Hi, I clustered more than 10,000 genes based on gene expression profile under different treatment conditions. I used the dynamic tree cut package in R. However, it produced around 90 clusters. How do I evalute the clustering results with such a high number of clusters? ...
gene expression clustering written 5 weeks ago by teabonng10 • updated 5 weeks ago by Jean-Karim Heriche16k
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dynamic tree cut
... Hi, I am clustering log2fold changes of genes. I am confused about the output of the dynamictreecut package. If I run the following: dynamic_hybrid = cutreeHybrid(clust_fc, as.matrix(dist_fc), deepSplit=1) clusters = dynamic_hybrid$labels how do I know which genes are assigned to which c ...
dynamictreecut clustering written 5 weeks ago by teabonng10 • updated 5 weeks ago by Jean-Karim Heriche16k
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Gene expression meta analysis
... Hi, I am analyzing independent RNA-Seq datasets and doing a meta analysis. Is it valid to compare global transcription profiles from multiple datasets based on the fold changes? For each RNA-Seq dataset, I normalize counts within each dataset and then calculate the fold changes of all genes relativ ...
transcription profiles gene expression written 8 weeks ago by teabonng10
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Identification of co-regulated genes by clustering
... Hi, I would like to identify clusters of co-regulated genes based on gene expression data under various treatment conditions. I am wondering how many of these treatment conditions, like how many experiments/datasets are needed to reliably determine these clusters. Will 10 datasets be enough? Thank ...
gene expression co-regulated genes clustering written 8 weeks ago by teabonng10
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Comment: C: edger model matrix design of linear model
... Hi, there is a big difference in the results. The results using the design <- model.matrix(~timepoint) makes much more biological sense. ...
written 9 weeks ago by teabonng10

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