User: rk489

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rk4890
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Posts by rk489

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Error in GEOquery
... Hi, I'm trying to download RNAseq data from the GEO dataset "GSE67835". However, I'm getting the following error:  Error in download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) :    cannot open URL 'http://www.ncbi.nlm.nih.gov/geo/query/acc. ...
geoquery R getgeo written 7 months ago by rk4890 • updated 7 months ago by James W. MacDonald45k
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Comment: C: getting a list of probe IDs from topTable (limma version 3.18.13)
... Thanks Aaron. rownames(top_table)  seems to work. However, I don't think its a problem of rpy2 because I'm using it at a lot of places in my code but it only gives error while indexing the top_table. Or maybe its a problem while indexing data frames? Thanks again!  ...
written 2.0 years ago by rk4890
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getting a list of probe IDs from topTable (limma version 3.18.13)
... I'm using limma to find differentially expressed genes in an affymetrix array. However, when I try to extract the probe ids after applying eBayes to lmfit using topTable (probe IDs are in the first column of the resulting data frame), it gives me the 2nd column of the data frame (which is logFC). If ...
limma rpy written 2.0 years ago by rk4890

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