User: Kasthuri

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Kasthuri240
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Posts by Kasthuri

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Comment: C: EdgeR differential expression and heatmap
... Thanks, I figured out. ...
written 9 weeks ago by Kasthuri240
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EdgeR differential expression and heatmap
... I performed a differential gene expression analysis for the red vs. blue group as shown in this image below (RNA-seq data) using TCGAbiolinks which uses the EdgeR package. Clearly, there is a difference between the groups however the difference is due to under-expression in **some** samples in the b ...
rna-seq written 9 weeks ago by Kasthuri240
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Comment: C: Error in GDCprepare
... Yes, it works for me and I processed my data. Hopefully, they shouldn't change the code at TCGAbiolinks. ...
written 10 weeks ago by Kasthuri240
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Comment: C: Error in GDCprepare
... Ok, I figured out. If we are using the new query as suggested, we need to use `geneInfo = geneInfoHT` option in the `TCGAanalyze_Normalization` function. Thus, it should be, Norm.Mat.C1 <- TCGAanalyze_Normalization(tabDF = Matrix.C1, geneInfo = geneInfoHT) However, using this updated prot ...
written 10 weeks ago by Kasthuri240
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Comment: C: Error in GDCprepare
... Thanks a lot, noorpratap.singh. However, I get errors down the line, now. listSamples <- Cluster.1.df$`Sample ID` library(SummarizedExperiment) query <- GDCquery(project = "TCGA-BRCA", data.category = "Transcriptome Profiling", data.t ...
written 10 weeks ago by Kasthuri240
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Comment: C: Error in GDCprepare
... Thanks! I updated it and still have problems. Here is the full query - it is exactly as posted in their [manual][1] library(TCGAbiolinks) library(SummarizedExperiment) # You can define a list of samples to query and download providing relative TCGA barcodes. listSamples &l ...
written 10 weeks ago by Kasthuri240
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Error in GDCprepare
... I am working with RNA seq data from TCGA using TCGAbiolinks. Everything has been working fine so far and suddenly I get this error: > RnaseqSE <- GDCprepare(query) |=================================================================================| 100% Error in fix.by(by.y, y) : ' ...
tcga written 10 weeks ago by Kasthuri240
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Comment: C: Does mitotic activity inversely correlate with HiC interactions data?
... Thanks! Yes, I realized the HiC interactions are mapped during interphase. This is my exact question: Let's say I capture some cells and do a HiC on it. If none of the cells is undergoing mitosis, and all of them have passed the mitotic stage, are the interactions reflective of underlying cell densi ...
written 7 months ago by Kasthuri240
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Does mitotic activity inversely correlate with HiC interactions data?
... At least at the outset, it appears if the interchromosomal interactions are higher as determined by HiC then we might expect lower mitotic activity and vice-versa. Can anyone confirm this or suggest relevant literature that validates/invalidates this hypothesis? Thanks! ...
next-gen written 7 months ago by Kasthuri240 • updated 7 months ago by Jean-Karim Heriche18k
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Comment: C: Expanding bed format into single nucleotide resolution
... Awesome! Thank you very much. ...
written 7 months ago by Kasthuri240

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