User: Maithê Barros
Maithê Barros • 10
- Reputation:
- 10
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- New User
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- Last seen:
- 5 months ago
- Joined:
- 1 year, 8 months ago
- Email:
- m******@hotmail.com
Posts by Maithê Barros
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... Awesome. Thank you so much!
...
written 5 months ago by
Maithê Barros • 10
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... There is no pairing or repetition, just 2 groups with 3 different individuals in each group.
I read a bunch of stuff about DESeq2 and I understood that when comparing two groups with different individuals, I would need to control for expected differences between individuals. That is the reason why ...
written 5 months ago by
Maithê Barros • 10
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... Hello,
I have to perform the differential gene expression analysis for 6 RNA-seq samples using DESeq2.
My colData looks like this:
sample tissue horse
sample_60.bam ex_vivo 1
sample_65.bam ex_vivo 2
sample_75.bam ex_vivo 3
sample_80.bam in_vivo ...
written 5 months ago by
Maithê Barros • 10
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... Many thanks for your reply, Michael. I had to step back from this analysis, but now I am back to it.
If I perform the analysis without controlling for horses, would that be correct? Taking into account that each group (follicular, luteal and anoestrous) have different horses?!
If so, would the cor ...
written 7 months ago by
Maithê Barros • 10
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... I have changed my metadata to:
sample,horse,phaseANDtimepoint
sample_1.bam,1A,follicular_0h
sample_2.bam,1A,follicular_24h
sample_3.bam,1A,follicular_48h
sample_4.bam,1B,follicular_0h
sample_6.bam,1B,follicular_48h
sample_7.bam,2C,follicular_0h
sample_8.bam,2C,follicular_24h
sample_9.bam,2C,follic ...
written 7 months ago by
Maithê Barros • 10
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... Hello,
I am doing RNA-seq analysis of DE genes from mare's endometrial biopsies. It is a timecourse experiment with samples at 0h, 24h and 48h across three different stages (follicular, luteal and anoestrous). I am having a hard time trying to figure out the design I should use and also having trou ...
written 8 months ago by
Maithê Barros • 10
• updated
8 months ago by
Michael Love ♦ 23k
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... Awesome! Thank you ever so much for your quick reply and for helping me out, Michael!
...
written 8 months ago by
Maithê Barros • 10
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... Thank you so much for the quick reply! I did think about it and I already ran something like that:
bam_exp3 <-c("sample_55.bam", "sample_56.bam", "sample_57.bam","sample_58.bam", "sample_59.bam", "sample_60.bam", "sample_61.bam", "sample_62.bam", "sample_63.bam", "sample_64.bam", "sample_65.bam" ...
written 8 months ago by
Maithê Barros • 10
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... Hello,
I am doing RNA-seq analysis of DE genes from mare's endometrial biopsies. We collected our samples at an abattoir due to restrictions with samples collected from live horses.
Thus, I have three time points: alive_0h (when the mare was just slaughtered, tissue representing the uterus of a ...
written 8 months ago by
Maithê Barros • 10
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... Thanks a lot for your reply, Michael. I have renamed my variables.I ran:
ddsLRT <- DESeqDataSet(se, design = ~ horse + timepoint)
ddsLRT <- estimateSizeFactors(ddsLRT)
ddsLRT <- estimateDispersions(ddsLRT)
ddsLRT <- nbinomLRT(ddsLRT, reduced = ~ horse)
resLRT <- results(ddsLRT)
table ...
written 20 months ago by
Maithê Barros • 10
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20 months ago,
created a question with more than 1,000 views.
For DESeq2 Time course analysis design - only time points WITHOUT treatments
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