User: morteza.hadizade

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Posts by morteza.hadizade

<prev • 16 results • page 1 of 2 • next >
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Timeout was reached error in GEOquery package
... Hi every one During microarray analysis, I encounter below error, rafter loading GEOquery package.   > gset <- getGEO(dataset, GSEMatrix =TRUE, AnnotGPL=TRUE, destdir = "C:/R Database/TGFb /Data/") Timeout was reached error: Connection timed out after 10000 milliseconds   How to resolve ...
microarray software error R written 20 days ago by morteza.hadizade10 • updated 20 days ago by Kevin Blighe30
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Comment: C: Remove NaN from a list or replace NaN with a value.
... Dear Dr Pickering, Thank you so much for your valuable guidance. ...
written 20 days ago by morteza.hadizade10
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Comment: C: Remove NaN from a list or replace NaN with a value.
... Hi Dr pickering, Thank you so much, your answer was reasonable and accurate. After downloading the latest version of github, the previous error has been resolved. But I had to change TRUE to FALSE (in below command) to analyze done. es_res <- es_meta(anals, by_source = FALSE) while source = ...
written 23 days ago by morteza.hadizade10
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Comment: C: Remove NaN from a list or replace NaN with a value.
... Hi Dr pickering, Thanks for your attention, library(crossmeta) library(shiny) gse_names  <- c("GSE87105", "GSE87108") get_raw(gse_names) esets <- load_raw(gse_names) # I select young samples as control and old samples as case, In both GSE number. anals <- diff_expr(esets) es_res &l ...
written 24 days ago by morteza.hadizade10
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Comment: C: Remove NaN from a list or replace NaN with a value.
... Name of the package is “crossmeta”. As shown in the error, “anals” contains missing value (Na), I remove NA with anals<- na.omit(anals), but I encountered an error in removing NaNs. ...
written 24 days ago by morteza.hadizade10
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Comment: C: Remove NaN from a list or replace NaN with a value.
... Hi Lluís, I'm sorry for the delay in replying, the lists include matrix, table, and character.   ...
written 25 days ago by morteza.hadizade10
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Remove NaN from a list or replace NaN with a value.
... Hi every one During microarray meta-analysis, I encounter below error, (“anals” class is a list). > es_res <- es_meta(anals, by_source = TRUE) Error in quantile.default(x, probs = c(0.25, 0.75)) :  missing values and NaN's not allowed if 'na.rm' is FALSE  please guide me, which one is more l ...
R meta-analysis written 25 days ago by morteza.hadizade10
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Comment: C: extracting the genes associated with the groups or samples in pheatmap.
... Hi Kevin, Thank you so much, your answer was reasonable and accurate. According to your guidance, If I want to extract a gene list, I should use the cutree command, in this command, can I use the sample number instead of the cluster number? I have 73 sample.     ...
written 9 weeks ago by morteza.hadizade10
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Comment: C: extracting the genes associated with the groups or samples in pheatmap.
... Dear Malcolm, Thank you I really appreciate your help. ...
written 9 weeks ago by morteza.hadizade10
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Comment: C: extracting the genes associated with the groups or samples in pheatmap.
... Hi, Thank you for pointing this out. these genes are reported in an article, I get those from a supplementary file, I want to compare the genes of each group with my results. The gene list published in the supplementary file was a matrix, I clustered it by creating a pheatmap, but I could not extra ...
written 10 weeks ago by morteza.hadizade10

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