User: Nithisha

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Nithisha10
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Posts by Nithisha

<prev • 33 results • page 2 of 4 • next >
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DEG with Limma without replicates and best plots to represent results
... Hi all, I have a few questions regarding Limma. 1) I am asking a question with reference to https://support.bioconductor.org/p/48601/#102609. This is a case where there are no replicates for samples, and we cannot run eBayes or toptable. I understand that running fit2$coefficients will bring out l ...
limma written 10 weeks ago by Nithisha10 • updated 10 weeks ago by Aaron Lun18k
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Comment: C: Using R for EnrichR analysis
... Hi Thokall, Thank you for your reply! It is Enrichr that I was talking about! ...
written 10 weeks ago by Nithisha10
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Comment: C: Using R for EnrichR analysis
... Hello Gordon, Thank you for your reply. I meant Enrichr ( http://amp.pharm.mssm.edu/Enrichr ). I think that Python can help get results from Enrichr eg. for a list of upregulated genes from DEG analysis, I can get enriched transcription factors, pathways, ontologies etc. I was wondering if I could ...
written 10 weeks ago by Nithisha10 • updated 10 weeks ago by Gordon Smyth32k
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Comment: C: limma topTable doesn't work without replicates [was: Help with limma]
... when fit2$coefficients is used, log2FC is displayed for each one of the samples. In this case, what is the reference sample which we can compare the logFC against?   Thanks ...
written 11 weeks ago by Nithisha10
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Using R for EnrichR analysis
... Hi everyone, Is there a specific package I can utilize in R to conduct EnrichR analysis for up-regulated  and down-regulated genes? While searching I have come across Python packages to do this but not in R. Any advice would be appreciated! Thanks ...
enrichr written 11 weeks ago by Nithisha10 • updated 10 weeks ago by thokall90
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Comment: C: Downloading microarray data for DEG analysis!
... That makes it very clear, thank you! appreciate it. ...
written 11 weeks ago by Nithisha10
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Comment: C: Best DEG tool for datasets with FPKM counts?
... Thank you for the information. ...
written 11 weeks ago by Nithisha10
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Answer: A: Best DEG tool for datasets with FPKM counts?
... Hi Steve, Thank you so much for your reply. When I do sample(dat$gebe_id, 20), I get this:  [1] Acot8         Tarm1         Aph1b          [4] Cga           Ptms          Irx3           [7] 1700003F12Rik Six3          Tdh           [10] Olfr67        Gm14327       Stx6          [13] Zfp868        ...
written 11 weeks ago by Nithisha10
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Best DEG tool for datasets with FPKM counts?
... Hi everyone, I have a dataset that contains FPKM values for 5 samples. Is it alright to carry out log2 transformation on these values and using Limma on them or is there a better way to do this? Also, my gene_id column contains something like this- 0610005C13Rik,  0610007L01Rik. Could anyone guide ...
fpkm written 11 weeks ago by Nithisha10
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Comment: C: Downloading microarray data for DEG analysis!
... Hi James, Thank you for your reply. I went through ?annotateEset and have a few questions that I hope are not too basic. 1) Firstly, what would be the difference between mogene10strranscriptcluster.db and pd.mogebe.1.0.st.v1? And how would I know to look for these packages within the library "affy ...
written 11 weeks ago by Nithisha10

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