User: landscape95

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landscape9570
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Posts by landscape95

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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 26 days ago by landscape9570
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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 28 days ago by landscape9570 • updated 27 days ago by theobroma22890
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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 28 days ago by landscape9570
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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 28 days ago by landscape9570 • updated 28 days ago by Santosh Anand2.9k
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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 weeks ago by landscape9570
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Map from GEO samples' name to TCGA name
... I am working on several GEO data sets, the samples are GSMxxx, can these samples be converted to TCGA format type TCGA-xx-xx. For example, data sets "GSE10810", "GSE10780", "GSE12276", "GSE19615", "GSE20711", "GSE21653", "GSE9195" on NCBI. Your help is really appreciated. Thank you! https://www.ncb ...
mapping written 5 weeks ago by landscape9570 • updated 5 weeks ago by Samuel Brady230
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Get mRNA, miRNA, lncRNA specific for probes
... I currently need to map the probe to their types of RNA (eg. mRNA, miRNA, lncRNA) on GEO data from Affymetrix Human Genome U133 Plus 2.0 Array. I found a page on NCBI presents the probes with corresponding information but I cannot control how to extract all of the data from their descriptions. I nee ...
geo written 5 weeks ago by landscape9570 • updated 5 weeks ago by Samuel Brady230
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Comment: C: how to select certain columns in R
... try to use "colnames, substr and which" functions in R ...
written 6 weeks ago by landscape9570
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Comment: C: Clinical data from GEO
... Thank you very much, Professor Istvan Albert ...
written 6 weeks ago by landscape9570
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Getting lncRNA from TCGA (Breast cancer BRCA type)
... Hello everyone, Does TCGA provide lncRNA from their own experience or we have to use to lncRNA from the third-party system like the former post here? https://www.biostars.org/p/202939/ Thank you every much! ...
lncrna written 6 weeks ago by landscape9570

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