User: Maithê Barros
Maithê Barros • 10
- Reputation:
- 10
- Status:
- New User
- Location:
- Last seen:
- 10 months, 1 week ago
- Joined:
- 2 years, 1 month ago
- Email:
- m******@hotmail.com
Posts by Maithê Barros
<prev
• 11 results •
page 1 of 2 •
next >
0
votes
1
answer
198
views
1
answers
... Awesome. Thank you so much!
...
written 11 months ago by
Maithê Barros • 10
0
votes
1
answer
198
views
1
answers
... 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 11 months ago by
Maithê Barros • 10
0
votes
1
answer
198
views
1
answer
... 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 11 months ago by
Maithê Barros • 10
0
votes
1
answer
324
views
1
answers
... 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 12 months ago by
Maithê Barros • 10
0
votes
1
answer
324
views
1
answers
... 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 13 months ago by
Maithê Barros • 10
0
votes
1
answer
324
views
1
answer
... 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 13 months ago by
Maithê Barros • 10
• updated
13 months ago by
Michael Love ♦ 25k
0
votes
1
answer
305
views
1
answers
... Awesome! Thank you ever so much for your quick reply and for helping me out, Michael!
...
written 13 months ago by
Maithê Barros • 10
0
votes
1
answer
305
views
1
answers
... 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 13 months ago by
Maithê Barros • 10
2
votes
1
answer
305
views
1
answer
... 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 13 months ago by
Maithê Barros • 10
0
votes
1
answer
2.4k
views
1
answers
... 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 2.1 years ago by
Maithê Barros • 10
Latest awards to Maithê Barros
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For DESeq2 Time course analysis design - only time points WITHOUT treatments
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 16.09
Traffic: 436 users visited in the last hour