User: osieman52

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osieman5220
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Posts by osieman52

<prev • 24 results • page 1 of 3 • next >
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Comment: C: Reasons for switching from Affymetrix HGU133Plus 2.0 array platform to HGU133Plu
... I think that thats a different topic by it self. ...
written 10 months ago by osieman5220
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Reasons for switching from Affymetrix HGU133Plus 2.0 array platform to HGU133Plus+PM
... Hi all, For my intership research I have to work with data from the Affymetrix platforms hgu133plus 2.0 and hgu133Plus+PM. As a general question I would like to know why would one switch from platforms. As far as I know there is lots of data available for the hgu133plus 2.0 platform. So what are t ...
genome micro-array affymetrix written 10 months ago by osieman5220
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Answer: A: how to make "custom" affy batch vector (affymetrix plus2)
... I think i found the answer to this myself . Unzip al .CEL files in to 1 directory and use this directory to read them in. `setwd("path/to/CEL/files")` `celfiles <- dir()` `vec <- makeVectorsAffyBatch(celfiles, batch.id ,etc...)` this should work. ...
written 11 months ago by osieman5220
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how to make "custom" affy batch vector (affymetrix plus2)
... Dear all, Using the frmatools library in R I would like to create own affybatch Vectors. I am using the makevectorsaffybatch() function for this but I am receiving the following errors using it: `vec <- makeVectorsAffyBatch(files = listWithCelFiles ,file.dir = fullPathToCelFiles,batch.id = re ...
software error R written 11 months ago by osieman5220
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Getting information about samples(.CEL files) from GEO using R
... Hello all, Using the `GEOquery` library in R I have managed to download 850 samples I am interested in. I used the following code for this: `x <- as.list(scan("fileWithGEOsampleAccesionCodes.txt", what ="" , sep = "" ))` `data= lapply(x,getGEOSuppFiles)` I have read the CEL files into an a ...
R micro-array written 12 months ago by osieman5220 • updated 12 months ago by Kevin Blighe37k
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Comment: C: Downloading multiple samples with GEO accesion numbers
... A small question added to this quetions, how would one find the batch IDs of the downloaded files? I want to create vectors in orderer to do this I need batch ids. How could I find or generate these batch ids ? ...
written 12 months ago by osieman5220
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Answer: A: Downloading multiple samples with GEO accesion numbers
... **Solution in R:** `library(GEOquery)` `x <- as.list(scan("files_with_GEO_accesionCodes.txt", what ="" , sep = "" ))` `files = lapply(x, getGEOSuppFiles)` ...
written 12 months ago by osieman5220
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Comment: C: Downloading multiple samples with GEO accesion numbers
... I managed to find an easy way to download the files I need by using R. library(GEOquery) x <- as.list(scan("files_with_GEO_accesionCodes", what ="" , sep = "" )) files = lapply(x, getGEOSuppFiles) Thank you for the responds! ...
written 12 months ago by osieman5220
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Comment: C: Downloading multiple samples with GEO accesion numbers
... Thanks for the link but, unfortunately this doesn't provide enough information to help me out. ...
written 12 months ago by osieman5220
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Downloading multiple samples with GEO accesion numbers
... Dear all, I have GEO accession numbers for 850 samples I would like to download. What is the easiest way to download a bulk of data from GEO database. I know that it can be done with a ftp or by using R (geoQuery). But I'am not sure how. Can someone please help me or give me advice on how to do ...
geo microarray written 12 months ago by osieman5220

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Scholar 12 months ago, created an answer that has been accepted. For A: Downloading multiple samples with GEO accesion numbers

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