User: Jon
Jon • 160
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... Thank you...........! ...
written 7 weeks ago by
Jon • 160
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... Hi,
I have RNA seq expected counts from RSEM (n=3, two conditions). I get only 50 differentially expressed genes from DESEQ2 (FRD<0.05),while I'm getting 160 differentially expressed genes from EBSEq (PPDE> 0.95, that means FDR<0.05). Even though they are different statistics, why they are ...
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C: edgeR gives no DE genes <0.05 FDR
... I removed each sample from each condition and looked at the PCA plots, there's an outlier in each condition. I will also try svaseq() to remove any batch effect if possible. Thanks for making me understand everything from this post . ...
written 7 weeks ago by
Jon • 160
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C: edgeR gives no DE genes <0.05 FDR
... Yes I understand, I used RSEM-coupled with-STAR to get expected counts from fastq files, Is there any way I can do some (pre-) processing make the data look good? ...
written 7 weeks ago by
Jon • 160
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C: edgeR gives no DE genes <0.05 FDR
... Okay, Here is log transformed count's PCA
![enter image description here][1]
[1]: https://i.ibb.co/hBRPC6z/Screen-Shot-2019-10-15-at-11-01-38-AM.png ...
written 7 weeks ago by
Jon • 160
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Comment:
C: edgeR gives no DE genes <0.05 FDR
... x<- read.table('/Users/sudharsankannan/desktop/pvrun/countsource/fcounts.txt', header=T, sep="")
##########################################edgeR ###################################
group <- factor(c(2,2,2,1,1,1,3,3,3))
y <- DGEList(counts=x,group=group)
keep <- filter ...
written 7 weeks ago by
Jon • 160
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352
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Comment:
C: edgeR gives no DE genes <0.05 FDR
... Thank you, here is my PCA
Reminder: I used edgeR, Three conditions triplicated.
![PCA plot][1]
[1]: https://i.ibb.co/xFhWW6b/norm.png ...
written 7 weeks ago by
Jon • 160
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352
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4
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Comment:
C: edgeR gives no DE genes <0.05 FDR
... Your comment is really valuable to me, I will try the ones you have mentioned ...
written 7 weeks ago by
Jon • 160
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8 follow
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... Hi
Why edgeR giving me no DE genes with FDR <0.05? What could be wrong with my dataset? I have used the same codes for other dataset, I get at least 50 DE genes with FDR <0.05.
Thanks in advance!
qlf2<- glmQLFTest(fit, coef=2)
cs <- topTags(qlf2, n=Inf, sort.by="PValue")$table ...
written 8 weeks ago by
Jon • 160
• updated
7 weeks ago by
Antonio R. Franco • 4.2k
0
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295
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Comment:
C: How to normalize my rna seq data?
... Thank you! I knew that edgeR does normalization inside it. So I used edgeR for differential expression analysis.
But I wan to show the DE genes in a heatmap, for that How can I normalize for that? (I prefer Z-score of normalized counts as it is he common in all the publication) ...
written 10 weeks ago by
Jon • 160
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