User: Do it!

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Do it!10
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Posts by Do it!

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Warning messages: gene set enrichment analysis with clusterProfiler
... Thank you so much! I will post it into Bioconductor for more tutorials. ...
written 5 hours ago by Do it!10
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Warning messages: gene set enrichment analysis with clusterProfiler
... Hello Dears, I was doing gene set enrichment analysis with a Bioconductor package **clusterProfiler** I am using window 10 and my R and Rstido are up-to-date but getting the following warnings while running KEGG gene set enrichment analysis. Here are Warning messages: 1: In preparePathwaysA ...
R clusterprofiler written 7 hours ago by Do it!10 • updated 6 hours ago by antonioggsousa910
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genes popup in the volcano plots
... Hi Dears, I am just curious about genes that popup, when you use enhanced volcano plots, are they appeared in the plot randomly or based on their level of significance? Thanks for the feedback! Best, AD ...
enchancedvolca written 9 days ago by Do it!10
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Comment: C: predicting some phenotype by gene
... @user_without_id, Hi, I think I wasn't put my question clearly for you to understand it well. I have four sample groups(A, B, C, D) and each sample groups has biological replicates. Sample Group A has 10 biological replicate, B= 8, C= 12, D= 10. Now I want to model a liner regression `lm(BMI~gene_i ...
written 16 days ago by Do it!10 • updated 3 days ago by RamRS28k
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Comment: C: predicting some phenotype by gene
... Thanks for your quick replay! It is bulk RNAseq and I have 50 samples. The number of individuals for group A 10, 8 for B group, 12 for group C and 10 for group D. ...
written 21 days ago by Do it!10
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predicting some phenotype by gene
... Hi Dear friends, Thank you so much for your constant help here. Today I would like to ask a question on linear regression analysis using limma. I have RNAseq data and expression profile is count. Whereas the phenotypic data is continuous data. I want to do linear regression to predict phenotypic fu ...
limm rna-seq written 21 days ago by Do it!10 • updated 3 days ago by Biostar ♦♦ 20
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enrichment analysis using cluster profiler
... Hello Guys, I would like to ask you on enrichment analysis result. I did KEEG hypergeometric test using a Bioconductor package **clusterprofiler**. pvalues was adjusted by **'none' with cutoff <0.5** and got a number of pathways on which most are interesting. Using **pvalue cutoff < 0.05** I ...
R biocondactor clusterprofiler written 28 days ago by Do it!10 • updated 28 days ago by Papyrus360
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Comment: C: How to download matrix of the "GSE73554"
... Hi Andrews, Thank you! Actually didn't get an error in my code and in your codes as well. What I am looking for in this "GSE73554" is the expression profile (the matrix of the expression profile like the list of genes in the rows and samples in the columns). Thanks! ...
written 5 weeks ago by Do it!10
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Comment: C: How to download matrix of the "GSE73554"
... Hi Matthew, Thank you for your answer. Actually didn't get an error in my code and in your codes as well. What I am looking for in this "GSE73554" is the expression profile (the matrix of the expression profile like the list of genes in the rows and samples in the columns). Thanks! ...
written 5 weeks ago by Do it!10
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How to download matrix of the "GSE73554"
... Hello, First of all, Thank you for your time and help! Could please give me some directions on how to download publicly available RNAseq data "GSE73554" I used command lines: KO_RF_GSE73554 <- download.file("https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi", "GSE73554_KO_RF_Intron_Exon_RFP.txt ...
tutorial rna-seq written 5 weeks ago by Do it!10 • updated 5 weeks ago by MatthewP690

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