User: gracie

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gracie10
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3 years, 2 months ago
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Posts by gracie

<prev • 13 results • page 1 of 2 • next >
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Comment: A: Affymetrix miRNA 4.0 Normalization
... Thank you, I will go with that most probably. ...
written 6 months ago by gracie10
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Comment: C: Affymetrix miRNA 4.0 Normalization
... As much as I know it should be in featureData part but it is empty it only says annotated dataframe. > str(rawData) Formal class 'ExpressionFeatureSet' [package "oligoClasses"] with 9 slots ..@ manufacturer : chr "Affymetrix" ..@ intensityFile : chr NA ..@ assay ...
written 6 months ago by gracie10
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Comment: C: Affymetrix miRNA 4.0 Normalization
... Thank you. The reason I want to extract human only probes is I thought rma results would differ between rma with all probesets vs only human. > rownames(rawData) [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" "15" "16" " ...
written 6 months ago by gracie10
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Comment: C: Affymetrix miRNA 4.0 Normalization
... Thank you for your answer but I could not find a way to filter rawdata with probeIDs. When I extract the row names with probeNames function (probeNames(rawData), it has 346085 probes however array expression data (rawData@assayData$exprs) has 292681 rows. ...
written 6 months ago by gracie10
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Comment: C: Affymetrix miRNA 4.0 Normalization
... Sure, [GeneChip miRNA 4.0][1] it is. There are probes for human mouse and rat. Since using all probes would change RMA and limma results I thought I should use only human probes. [1]: https://www.thermofisher.com/order/catalog/product/902412 ...
written 6 months ago by gracie10
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Affymetrix miRNA 4.0 Normalization
... I am analyzing a GeneChip miRNA 4.0 Array dataset. here is my code; library(oligo) library(pd.mirna.4.0) celFiles <- list.celfiles( full.names=TRUE) rawData <- read.celfiles(celFiles, pkgname="pd.mirna.4.0") eset <- rma(rawData) This gives results for all organism. Is ...
microarray mirna written 6 months ago by gracie10
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Gene Set Enrichment between two dataset
... Dear all, I want to perform gene set enrichment analysis between two datasets. There are packages for GO or KEGG pathway enrichment but I could not find one to calculate enrichment score between user given geneset and genelist. Is there any package for that? Thank you ...
r language gsea rna-seq written 14 months ago by gracie10 • updated 14 months ago by ewre220
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pathway analysis tools
... Hi, I looking for tools for the pathway analysis; upstream and downstream analysis and/or pathway enrichment for high-throughput data similar to ingunity pathway analysis. It doesn't have to be freeware yet I want more comprehensive tool especially suitable for miRNA analysis. ...
ipa mirna written 2.1 years ago by gracie10 • updated 2.1 years ago by Denise - Open Targets5.0k
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CNA vs mRNA Expression level
... Hi, I am comparing CNA data with mRNA expression level. For some genes there is no correlation between copy number and mRNA expression level and even for some there is negative relation (low copy number yet high mRNA expression). I found some papers stating same situation but I could not find any ...
cna tcga written 2.2 years ago by gracie10 • updated 22 months ago by igor8.6k
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Comment: C: Trying to check plasmid alignment
... Thanks, it worked . ...
written 2.3 years ago by gracie10

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Popular Question 12 months ago, created a question with more than 1,000 views. For pathway analysis tools

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