User: Do it!
Do it! • 10
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Posts by Do it!
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... 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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... 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 ...
written 7 hours ago by
Do it! • 10
• updated
6 hours ago by
antonioggsousa • 910
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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 ...
written 9 days ago by
Do it! • 10
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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 ...
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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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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 ...
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... 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 ...
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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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... 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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... 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 ...
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