User: Maithê Barros

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Posts by Maithê Barros

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Comment: C: DESeq2 analysis design - different individuals for all samples
... Awesome. Thank you so much!  ...
written 3 months ago by Maithê Barros10
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Comment: C: DESeq2 analysis design - different individuals for all samples
... 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 3 months ago by Maithê Barros10
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DESeq2 analysis design - different individuals for all samples
... 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 ...
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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 5 months ago by Maithê Barros10
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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 5 months ago by Maithê Barros10
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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 6 months ago by Maithê Barros10 • updated 6 months ago by Michael Love22k
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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 6 months ago by Maithê Barros10
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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 6 months ago by Maithê Barros10
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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 6 months ago by Maithê Barros10
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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 18 months ago by Maithê Barros10

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Popular Question 18 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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