User: landscape95

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landscape9590
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Posts by landscape95

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Error with getGEO from GEOquery package bioconductor
... Hello everyone, I am trying to download the matrix file of GSE37405 but I got the error like in this picture, could anyone please help me how to fix this? your help is really appreciated! my code is simple just: library(GEOquery) setwd("./CanProg/") GSE37405 <- getGEO(GEO = "GSE37 ...
geoquery written 4 weeks ago by landscape9590 • updated 29 days ago by Sean Davis24k
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Comment: C: GEO data preprocessing with fRMA, limma and sva packages
... Thank you. I have another question on "using the limma and fRMA libraries to obtain log2-normalized expression signals for each probe set". Did I do it right in the code, would you please have a look in my code? I am not sure about 2 lines: data.matrix = frma(data.raw) and RNAdata_s ...
written 3 months ago by landscape9590
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Comment: C: GEO data preprocessing with fRMA, limma and sva packages
... Thank you very much, I fix the code to this, could you have a comment? Pheno contains 3 columns, for example: "GSM272133 1 normal" is the sample GSM272133 comes from my first GEO data set GSE10780 (I mark it as 1) and it is a normal sample. "GSM272972 2 cancer" is the sample GSM272972 comes from my ...
written 3 months ago by landscape9590
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Comment: C: GEO data preprocessing with fRMA, limma and sva packages
... Thank you, the thing is I don't know how to set the batch values as the paper's description: "using tumor vs normal as covariate". Could you give me some idea? ...
written 3 months ago by landscape9590
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GEO data preprocessing with fRMA, limma and sva packages
... Hello, everyone, I am trying to reproduce the lncRNA get from the paper "Portraying breast cancer with lncRNAs" by Olivier et. al. Here I came to the reproducing step: ![enter image description here][1] I don't know whether my code is doing right, can someone give me your comment? # load ...
geo written 3 months ago by landscape9590 • updated 3 months ago by lessismore380
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Probes - to - genes expression analysis question
... Why do people often map probes to genes names when we do analysis based on expression matrix? is it ok if we do the analysis such as subtyping cancer type based on probes? Thank you! ...
affymetrix written 4 months ago by landscape9590
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Question on number of probes in CEL and SOFT from GEO
... Hello everyone, I wonder why there is a different between the number of probes after I process the data from GEO in CEL compared to SOFT files. For example, data set GSM272923 just have 18382 probes as described in the table near the end of the page while as I downloaded CEL file, there were 54675 p ...
geo written 4 months ago by landscape9590 • updated 4 months ago by theobroma221.0k
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Compare between microarray data sets
... Hello, everyone, I downloaded 6 data sets from GEO but they are not in the same form of normalisation, now I want to combine to the expression matrix to compare the expression data. Should I re-normalize the data again and how should I do it? Is it possible to compare those time in log2 normalisatio ...
microarray written 4 months ago by landscape9590
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Downloading from GEO
... I am downloading some GSE data sets from GEO NCBI but the speed is too slow 155KB/s, does anyone know other ways to download the raw CEL files? Thank you! For example this link of GSE9195: [https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE9195&format=file][1] [1]: https://www.ncbi.nlm.nih. ...
geo written 4 months ago by landscape9590 • updated 4 months ago by Santosh Anand3.0k
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Comment: C: Get mRNA, miRNA, lncRNA specific for probes
... Thank you, do we have a tool in R to help to convert to gene type? just like "gene type" in here: > [Gene Symbol: HSPA6] [Locus Tag: ] [Chromosome: 1] [Map Location: 1q23.3] [Description: heat shock protein family A (Hsp70) member 6] > [Gene Type: protein-coding] ...
written 5 months ago by landscape9590

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