User: Jon

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Jon160
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Posts by Jon

<prev • 129 results • page 1 of 13 • next >
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Comment: C: Why EBSEQ and DEseq2 gives different number of DE genes
... Thank you...........! ...
written 7 weeks ago by Jon160
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Why EBSEQ and DEseq2 gives different number of DE genes
... 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 ...
gene R alignment rna-seq written 7 weeks ago by Jon160 • updated 6 weeks ago by swbarnes27.0k
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Comment: 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 Jon160
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Comment: 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 Jon160
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Comment: 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 Jon160
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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 Jon160
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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 Jon160
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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 Jon160
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edgeR gives no DE genes <0.05 FDR
... 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 ...
software error R alignment rna-seq written 8 weeks ago by Jon160 • updated 7 weeks ago by Antonio R. Franco4.2k
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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 Jon160

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Popular Question 29 days ago, created a question with more than 1,000 views. For BWA MEM vs BOWTIE2 , which is best?
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Popular Question 8 weeks ago, created a question with more than 1,000 views. For BWA MEM vs BOWTIE2 , which is best?
Great Question 11 weeks ago, created a question with more than 5,000 views. For how to sum up the columns to remove the duplicated row names in RSEM output?
Popular Question 4 months ago, created a question with more than 1,000 views. For BWA MEM vs BOWTIE2 , which is best?
Popular Question 6 months ago, created a question with more than 1,000 views. For BWA MEM vs BOWTIE2 , which is best?
Popular Question 6 months ago, created a question with more than 1,000 views. For bwa mem has more MAPQ values as 0 and 60
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Popular Question 19 months ago, created a question with more than 1,000 views. For How to get --transcript-to-gene-map in RSEM?
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Popular Question 19 months ago, created a question with more than 1,000 views. For how to sum up the columns to remove the duplicated row names in RSEM output?
Popular Question 19 months ago, created a question with more than 1,000 views. For converting paired end reads to single end, is this a good idea?
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