User: Maithê Barros

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Posts by Maithê Barros

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Comment: C: RNA-seq time course experiment - DESEq2 Contrasts
... 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 Barros0
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Comment: C: RNA-seq time course experiment - DESEq2 Contrasts
... 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 Barros0
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RNA-seq time course experiment - DESEq2 Contrasts
... 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 ...
deseq2 interactions contrast rna-seq written 8 weeks ago by Maithê Barros0 • updated 8 weeks ago by Michael Love20k
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Comment: C: RNA-seq time course experiment - LRT design hep
... Awesome! Thank you ever so much for your quick reply and for helping me out, Michael!  ...
written 8 weeks ago by Maithê Barros0
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Comment: A: RNA-seq time course experiment - LRT design hep
... 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 Barros0
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RNA-seq time course experiment - LRT design hep
... 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 ...
timecourse deseq2 lrt written 8 weeks ago by Maithê Barros0
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Comment: C: DESeq2 Time course analysis design - only time points WITHOUT treatments
... 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 Barros0
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DESeq2 Time course analysis design - only time points WITHOUT treatments
... 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 ...
deseq2 rna-seq multiple time points written 14 months ago by Maithê Barros0 • updated 14 months ago by Michael Love20k

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Popular Question 14 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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