User: Maithê Barros

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Posts by Maithê Barros

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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 1 day 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 4 days ago by Maithê Barros0 • updated 4 days ago by Michael Love19k
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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 7 days 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 7 days 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 7 days 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 13 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 13 months ago by Maithê Barros0 • updated 13 months ago by Michael Love19k

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