User: tpm

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tpm10
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Posts by tpm

<prev • 37 results • page 1 of 4 • next >
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Comment: C: Input file for CompareCluster in ClusterProfiler
... Great to know that it helped :) ...
written 6 weeks ago by tpm10
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Answer: C: Input file for CompareCluster in ClusterProfiler
... Hi. Maybe this will in someway help you, I figured to explain from my codes and the idea will weave together at the end. If it will help you feel free to use it. In the example shown from this code, your A, was my excel sheet with ENTREZID and its corresponding logFC [(fold change)] My initial inpu ...
written 6 weeks ago by tpm10
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Comment: C: How to run protein-protein interaction on R using STRING database
... Its better to check on the website on installations: anyhow if you run this code it will work, if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("STRINGdb") ...
written 9 weeks ago by tpm10
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Answer: C: compareCluster error: On clusterProfiler DEGs enrichments analysis
... I realized the mistake, which was here 'EC17WT' as I have identical names. I had to change one of them: So not like this $EC17WT [1] "947315" "944895" "947758" "947761" "946796" "948517" $EC17WT [1] "947315" "944895" "947758" "947761" "946796" "948517" but like this: ...
written 3 months ago by tpm10
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compareCluster error: On clusterProfiler DEGs enrichments analysis
... I am working on Clusterprofiler. I am comparing 4 gene sets. I encountered an error, and I am trying to figure out what could be the problem when I run the compareCluster function. I do not know how I can solve this issue. > lapply(LISTcutoff5, head) $EC11WT [1] "947315" "944895" "94 ...
R bioconductor degs clusterprofiler written 3 months ago by tpm10
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Comment: C: How to pull logFC values for a select ENTREZID from a gene-list on R?
... Million thank you. I honestly did not know I could use StackOverflow. I am still a newbie on R :)). Thank you for the clarity. ...
written 3 months ago by tpm10
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Comment: C: How to pull logFC values for a select ENTREZID from a gene-list on R?
... If I may ask, a follow up question, how about if my gene list looks like this, how can I extract the desired list of genes from this kind of dataframe: `head(genelist)` ENTREZID FC 1 947315 1.576377015 2 944895 -0.023717866 3 947758 -0.125816872 4 947 ...
written 3 months ago by tpm10
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(Closed) Transform gene ID list to sentence seperated by comma as in example shown below.
... Hi all, I am new in bioinformatics and I want to simple transform my gene list with many rows (~100) from something like this: 948683 947293 947227 To something like this: 948683,947293,947227 either on R or command line, I don't know which is easier. ...
commandline R code written 3 months ago by tpm10
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Comment: C: How to pull logFC values for a select ENTREZID from a gene-list on R?
... Thank you very much. ...
written 3 months ago by tpm10
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How to pull logFC values for a select ENTREZID from a gene-list on R?
... Hello, I am working on R using the compareCluster package. I have a gene list like this (with ENTREZID on top and logFC at the bottom): `head(genelist)` 949101 945316 945807 947239 946699 945783 945780 94603 4.311420437 3.762809441 3.529820947 ...
R bioconductor dep written 3 months ago by tpm10

Latest awards to tpm

Scholar 3 months ago, created an answer that has been accepted. For C: compareCluster error: On clusterProfiler DEGs enrichments analysis

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