User: Kim

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Kim10
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1 year ago
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1 year, 2 months ago
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Posts by Kim

<prev • 22 results • page 1 of 3 • next >
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Comment: C: REACTOME and Ingenuity Pathway Analysis have inconsistent results
... Hi Thank you for your answer. I don't have a bioinformatic background so it's surprising (and also frustrating) to me to see the result inconsistent. I think the knowledgebase is freely accessible and they would have that in common, just the algorithms are different, so the results shouldn't be too ...
written 12 months ago by Kim10
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REACTOME and Ingenuity Pathway Analysis have inconsistent results
... Hello everyone I have a lists of genes for human and mouse. For the human gene list, I previously used REACTOME (https://reactome.org/) for pathway analysis. However, as this tool is only available for human, I later have a license to use Ingenuity Pathway Analysis (IPA) to do pathway analysis for ...
inconsistent result reactome ipa pathway analysis written 12 months ago by Kim10 • updated 12 months ago by Buffo1.8k
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Comment: C: Parsing error when loading microarray data from GEO
... It's still doesn't work mart <- useMart(host="useast.ensembl.org", + biomart="ENSEMBL_MART_ENSEMBL") Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached: Connection timed out after 10000 milliseconds I downloaded the GPL files and real ...
written 12 months ago by Kim10
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Comment: C: Parsing error when loading microarray data from GEO
... Thanks Kevin. This command works. But now I'm stuck at this: mart <- useMart('ENSEMBL_MART_ENSEMBL') Time-out error. I guess it has something to do with the ftp connection again. But I can download the GPL file from GEO. I'm thinking of using the GPL file for annotation. Do you know how I c ...
written 13 months ago by Kim10
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Comment: C: Parsing error when loading microarray data from GEO
... I'm not running R on a cluster, but on a computer of my institution in Germany. The institution network blocks access to ftp sites so I cannot get files directly from GEO. I restarted R and tried your codes but the result is still unchanged. I don't know if the ftp blockage affects the SOFT file whe ...
written 13 months ago by Kim10
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Comment: C: Parsing error when loading microarray data from GEO
... Hello Kevin Thank you very much for your reply. I could never get data directly from GEO. It's always like this: > gset <- getGEO("GSE61659", GSEMatrix =TRUE, getGPL=FALSE)[[1]] Error in open.connection(x, "rb") : Timeout was reached: Connection timed out after 10000 millisecon ...
written 13 months ago by Kim10
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Comment: C: Parsing error when loading microarray data from GEO
... Edited. Thank you. I'm quite new to this community :) ...
written 13 months ago by Kim10
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Parsing error when loading microarray data from GEO
... Hello everyone I try to load microarray data from GEO to R (I download the files to my computer then load it to R), but whether I use Matrix file or SOFT file, there's always this parsing error (following code and result). Despite the parsing errors, when I draw the boxplot with this data, the resu ...
geo matrix file parsing error microarray soft file written 13 months ago by Kim10
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Find the most frequently appeared genes in a list of pathways and genes
... Hello everyone I have a list of pathways and genes involved in those pathways as follow (the real list is much longer): ![enter image description here][1] I want to see which genes appear most frequently in these pathways. Do you know how to do that in R or recommend any tools? Thank you very mu ...
pathway dominant most frequent gene written 13 months ago by Kim10 • updated 13 months ago by zx87549.6k
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Comment: C: Extracting gene symbols from gene assignments in exon array data
... Hi Russ I tried this command and it works. Thank you :) for (i in 1:11005) { Gene_symbol[i] <- strsplit(full_table$gene_assignment, " // ")[[i]][2] } ...
written 13 months ago by Kim10

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