User: salamandra

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salamandra0
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Posts by salamandra

<prev • 16 results • page 1 of 2 • next >
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biomaRt expected a character string of length 1
... Hi, I'm getting this error: Error in getBM(attributes = c(micrTypeFilter, "ensembl_gene_id"), filters = micrTypeFilter, : The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this on the support site at http://su ...
biomart written 22 days ago by salamandra0 • updated 22 days ago by James W. MacDonald52k
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How to convert dataframe into ExpressionSetIllumina / summarized data with beadarray package?
... In documentation (beadsummary.pdf) of [beadarray][1] package it explains how to get a ExpressionSetIllumina from data deposited on GEO. Something like: library(GEOquery) url <- "ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE33126/" filenm <- "GSE33126_series_matrix.txt.gz" ...
beadarray written 5 weeks ago by salamandra0 • updated 5 weeks ago by Mark Dunning1.1k
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Comment: C: When applying rma to featureset get error: 'package' must be of length 1
... Thank you for your answer. The idea is to apply the same normalization method to several microarray raw data from several studies. I wanted to do it on affymetrix, illumina and agilent data. Do you know a normalization method that can be applied to these three platforms or at least applied to both a ...
written 6 weeks ago by salamandra0
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When applying rma to featureset get error: 'package' must be of length 1
... I am trying to apply `rma` from `oligo` package into data of file `GSE22247_non-normalized_data.txt` from this study: [GSE22247][1] Did: # read txt file into dataframe: rawtxt <- read.delim(paste0(txtpath), sep='\t', skip = 4, header = T) # convert dataframe into expression set: ...
biobase geoquery oligo written 6 weeks ago by salamandra0 • updated 6 weeks ago by James W. MacDonald52k
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Is there a way to save and open an expression set?
... I know we can save phenotype, feature and expression data of a expression set separately in a text files. I want to know if it's possible to save the expression set into a folder and then open it later for other applications? ...
biobase written 6 weeks ago by salamandra0 • updated 6 weeks ago by Kevin Blighe390
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Comment: C: Error object and replacement value dimnames differ, when changing column names o
... it was easier than I though. thank you! ...
written 7 weeks ago by salamandra0
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Error object and replacement value dimnames differ, when changing column names of assayData of ExpressionSet (although dimension is same)
... I retrieved raw expression values from [geo series][1] supplementary files and did a normalization: treatment1Samples <- c("GSM437316","GSM437286","GSM437305","GSM437297","GSM437277","GSM437282","GSM437269","GSM437302") treatment2Samples <- c("GSM437147","GSM437138","GSM437311","GSM43 ...
geoquery oligo expressionset written 7 weeks ago by salamandra0 • updated 7 weeks ago by James W. MacDonald52k
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Comment: C: DEseq2: Is vst/rlog transformation applied to raw counts or normalised counts?
... Thanks. So, counts are not scalled by row/mean gene expression (unlike the normalized counts for differential expression analysis)? Is it ok to subtract rlog values by log of mean expression of each gene before doing dendrogram, then? ...
written 11 months ago by salamandra0
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deseq2: use blind=T or blind=F when find gene groups?
... Hi, I'm using reduced model to get genes that vary over different conditions and using degPaterns() to split those genes into groups according to their expression pattern (code bellow). What want to know is in this case, should we use parameter blind=T or blind=F in rlog() ? Table <- data.fram ...
deseq2 rlog transformation written 11 months ago by salamandra0 • updated 11 months ago by Michael Love26k
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Comment: C: DEseq2: Is vst/rlog transformation applied to raw counts or normalised counts?
... Honestly even after reading manual pages I don't understand cause of the statistical terms. I'm trying to learn more on that area though. So, it means vst/rlog 'correct' for library size, but still dind't get if they correct for average gene expression across samples. And also, in this case should ...
written 11 months ago by salamandra0

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Popular Question 11 months ago, created a question with more than 1,000 views. For What are out-of-bound ranges? Is it necessary to get rid of them?

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