User: microbiotaiota

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Posts by microbiotaiota

<prev • 30 results • page 1 of 3 • next >
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Comment: C: Is there a program to average read counts from technical replicates?
... That makes sense, thank you. I will sum the reads in that case. ...
written 7 days ago by microbiotaiota20
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Comment: C: Is there a program to average read counts from technical replicates?
... Thank you. I will try that! ...
written 7 days ago by microbiotaiota20
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Comment: C: Is there a program to average read counts from technical replicates?
... Yes same biological sample, wouldn't averaging be more appropriate? Concatenating the two technical seems to be a lot easier. ...
written 7 days ago by microbiotaiota20
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Is there a program to average read counts from technical replicates?
... I have cell lines where RNA was extracted and was split across two lanes giving me two technical replicates per sample. I have my read counts for each technical replicate and I am going to use edgeR to get a DEG list. Is there a program which will average the reads from the technical replicates? Tha ...
rna-seq edger written 7 days ago by microbiotaiota20
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Comment: C: Suggestions on Labtop Mac for Bioinformatics
... Also note that newer Apple laptops will move to ARM architecture, i.e. they'll no longer be running on Intel processors. Back when Macs moved from PowerPC to Intel there were a couple of issues, this was from what I've heard from peers. ...
written 6 weeks ago by microbiotaiota20
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Comment: C: Clarity for proper design model matrix with paired sample analysis
... This [question/answer][1] on biostars might be helpful. [1]: https://www.biostars.org/p/258956/#259072 ...
written 8 weeks ago by microbiotaiota20
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Comment: C: EdgeR - comparison between subjects is not working
... I should have written that and I'll add it to the original post. I am trying to find 3 things: 1. DE genes in healthy individuals 2. DE genes in obese individuals 3. DE genes between healthy and obese individuals I have used `makeContrasts` and it works, however I didn't know how to account that ...
written 9 weeks ago by microbiotaiota20
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Comment: C: EdgeR - comparison between subjects is not working
... From what I understood in the vignette, in the examples they had 9 paired samples (9 patients) and 3 different conditions (healthy, disease1, disease2) so when doing `glmQLFTest` (as with below) I think the first nine 0's correspond to the nine patients and the last three values `0,-1,1` correspond ...
written 9 weeks ago by microbiotaiota20
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EdgeR - comparison between subjects is not working
... I have paired samples from cancer patients who were obese or not obese (labelled 'healthy'). Using 3.5 in edgeR to compare within and between samples. I am able to compare within a condition i.e. comparing tumour to control in healthy patients or comparing tumour to control in obese patients. I am ...
rna-seq edger written 9 weeks ago by microbiotaiota20
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Comment: C: Normalisation of paired samples in edgeR
... Great, thank you. Just saw this. I'll give this a go. ...
written 10 weeks ago by microbiotaiota20

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