User: Biologist

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Biologist190
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Posts by Biologist

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Comment: C: Question regarding immature transcripts with Ribo-zero RNA-seq data
... I didn't ask about the pipeline...my question is I found immature transcripts in my data. I would like to know whether such data can be used for novel lncRNA detection. ...
written 6 days ago by Biologist190
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Problem with edgesfile into cytoscape for network plot
... I was using 30,000 protein-coding genes and lncRNAs for network construction on WGCNA. I have got 25 modules. And I'm interested in creating a network plot. I see that everyone is using cytoscape. So, I got the edges and nodes files with the following commands. genes = colnames(datExpr) dim ...
wgcna cytoscape rna-seq R written 4 months ago by Biologist190 • updated 4 months ago by andres.firrincieli960
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Comment: C: Problem with differential analysis between two groups having low raw counts
... Thanks a lot for the information. Yes, actually when I took all the genes long with novel lncRNA transcripts and performed DEG analysis. And what I see is there re no novel lncRNA transcripts among DEGs I got. What I'm interested in is differentially expressed novel lncRNA transcripts. And ofcourse ...
written 6 months ago by Biologist190
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Comment: C: Problem with differential analysis between two groups having low raw counts
... @geek_y and @ATpoint Could you please check my below comment and tell me your opinion.thanq ...
written 6 months ago by Biologist190
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Comment: C: Problem with differential analysis between two groups having low raw counts
... Yes, I added `lib.size` for `cpm`. I'm afraid that we if I merge these novel transcripts with mRNA and Known lncRNAs, I won't be able to detect any novel differentially expressed transcripts. Because mRNAs are high expressed and lncRNAs are low expressed. I see that library sizes of the samples is ...
written 6 months ago by Biologist190
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Comment: C: Problem with differential analysis between two groups having low raw counts
... From the pipeline [lncRNApipe][1] I used, to detect novel lncRNAs....I found approx 10,000 novel lncRNA transcripts. And this is what I used with edgeR for GroupA vs GroupB comparison. Don't know what else I should use. [1]: https://github.com/biocoder/Perl-for-Bioinformatics/blob/master/NGS-U ...
written 6 months ago by Biologist190
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Comment: C: Problem with differential analysis between two groups having low raw counts
... These 10,000 lncRNA transcripts were novel transcripts in my analysis. So, yes I used `cpm` only. ...
written 6 months ago by Biologist190
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Comment: C: Problem with differential analysis between two groups having low raw counts
... I'm interested in only lncRNAs. I don't think it is wrong. ...
written 6 months ago by Biologist190
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Comment: C: Problem with differential analysis between two groups having low raw counts
... thank you...I actually used Filtering step from `edgeR` already like `keep <- rowSums(cpm(y) > 1) >= sample number`. With these among 10,000 I kept around 7000 lncRNA transcripts which are used for DEA. In there is other transcript in below box plot Is this still said as upregulated in Gro ...
written 6 months ago by Biologist190
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Problem with differential analysis between two groups having low raw counts
... Dear all, I have 40 liver cancer samples. Among them I have two groups. GroupA (26 samples) and GroupB (14 samples) and I have a total of 10,000 lncRNA transcripts. I'm trying to do differential analysis between GroupA vs GroupB using `edgeR`. With edgeR analysis I see that there are around 300 up ...
differential analysis expression rna-seq edger written 6 months ago by Biologist190 • updated 6 months ago by ATpoint40k

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Popular Question 9 weeks ago, created a question with more than 1,000 views. For Is logCPM expression data good for plottinng?
Popular Question 4 months ago, created a question with more than 1,000 views. For Is logCPM expression data good for plottinng?
Popular Question 5 months ago, created a question with more than 1,000 views. For Gene set enrichment analysis with edgeR output
Popular Question 5 months ago, created a question with more than 1,000 views. For Gene set enrichment analysis with edgeR output
Popular Question 7 months ago, created a question with more than 1,000 views. For Gene set enrichment analysis with edgeR output
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Popular Question 10 months ago, created a question with more than 1,000 views. For Differential analysis between two cell lines
Popular Question 12 months ago, created a question with more than 1,000 views. For Gene set enrichment analysis with edgeR output
Popular Question 12 months ago, created a question with more than 1,000 views. For Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
Popular Question 14 months ago, created a question with more than 1,000 views. For Gene set enrichment analysis with edgeR output
Popular Question 16 months ago, created a question with more than 1,000 views. For Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
Popular Question 16 months ago, created a question with more than 1,000 views. For Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
Popular Question 16 months ago, created a question with more than 1,000 views. For Gene set enrichment analysis with edgeR output
Popular Question 16 months ago, created a question with more than 1,000 views. For Identifying differentially expressed lncRNA's from RNA-Seq data
Popular Question 17 months ago, created a question with more than 1,000 views. For Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
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Popular Question 19 months ago, created a question with more than 1,000 views. For Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
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Popular Question 21 months ago, created a question with more than 1,000 views. For Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
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Centurion 2.2 years ago, created 100 posts.

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