User: Rob

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Rob30
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11 hours ago
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7 months, 3 weeks ago
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Posts by Rob

<prev • 112 results • page 1 of 12 • next >
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Comment: C: IPA pathway for DESeq2 result
... Thanks swbarnes2. Isn't this shrinkage fold change? ...
written 14 hours ago by Rob30
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IPA pathway for DESeq2 result
... Hi friends, I want to run pathway analysis with IPA for result of `DESeq2` for genes with `FDR < 0.05`. Which one should I use : `log2FoldChange` or `lfcSE` to run the pathway analysis? What are the difference between these two? ...
gene sequence written 17 hours ago by Rob30
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Comment: C: GSEA from broad institute normalization method
... Thanks Kevin. it was helpful. ...
written 17 hours ago by Rob30
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Comment: C: GSEA from broad institute normalization method
... Thanks for explanation When I used this I get error: counts(dds, normalized = TRUE) Error in .local(object, ...) : first calculate size factors, add normalizationFactors, or set normalized=FALSE how can I solve this? ...
written 1 day ago by Rob30
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Comment: C: GSEA from broad institute normalization method
... Thanks Kevin What I understand from your answer is : first I do DESeq work flow with the raw count data, then the result (`dds`) as the normalized count will come to `vst()` or `rlog()`: varStabilised <- vst(dds, blind = FALSE) Then this `varStabilised` will be my normalized data for GSE ...
written 1 day ago by Rob30
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Comment: C: GSEA from broad institute normalization method
... Hi I am trying to normalize my count data to do GSEA. these error come up: what is the solution? data <- read.csv("myData.csv") data <- matrix(data) vst(data) Error in vst(data) : less than 'nsub' rows, it is recommended to use varianceStabilizingTransformation di ...
written 2 days ago by Rob30
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Comment: C: HT-Seq count data
... Thanks ATpoin This worked great ...
written 2 days ago by Rob30
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GSEA from broad institute normalization method
... Hi freinds I have HT-Seq raw count data of 19000 coding genes and 300 samples of two groups (treatment and control). I want to do gene set enrichment analysis with GSEA from broad institute. do I need to normalize my data before GSEA? How should I normalize for this purpose? Thanks ...
rna-seq written 2 days ago by Rob30 • updated 2 days ago by Kevin Blighe69k
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HT-Seq count data
... Hi friends How should I split my data of 500 patients with RNA seq data into 2/3 training and 1/3 validation sets randomly? I tried to select randomly in excel, but result gives repeated patients in my sets. How can I use randomly without having duplicate patients? ...
rna-seq written 7 days ago by Rob30
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TCGAbiolinks HT-Seq count
... Hi friends I downloaded RNA seq and its related clinical data from biolink. with this code I get clinical data but when I use write.csv(clinical, clinical) the result file is messy and columns data are mixed. How can I get the clinical file correctly? this is my code: library(TCGAbiolinks) ...
gene rna-seq written 8 days ago by Rob30

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Centurion 4 weeks ago, created 100 posts.
Supporter 3 months ago, voted at least 25 times.

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