User: Maithê Barros
Maithê Barros • 0
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Posts by Maithê Barros
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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 4 weeks ago by
Maithê Barros • 0
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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 weeks ago by
Maithê Barros • 0
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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 weeks ago by
Maithê Barros • 0
• updated 8 weeks ago by
Michael Love ♦ 20k
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... Awesome! Thank you ever so much for your quick reply and for helping me out, Michael!
...
written 8 weeks ago by
Maithê Barros • 0
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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 weeks ago by
Maithê Barros • 0
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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 weeks ago by
Maithê Barros • 0
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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 14 months ago by
Maithê Barros • 0
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... Hello,
I am doing RNA-seq analysis of differential gene expression from mare's endometrial biopsies. I do not have any treatments though, and this is the reason I am having a hard time trying to figure out the design I should use as all examples I found so far had treatments + time points.
I have ...
written 14 months ago by
Maithê Barros • 0
• updated 14 months ago by
Michael Love ♦ 20k
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14 months ago,
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For DESeq2 Time course analysis design - only time points WITHOUT treatments
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