User: aristotele_m

gravatar for aristotele_m
aristotele_m30
Reputation:
30
Status:
New User
Location:
Italy
Last seen:
2 years, 6 months ago
Joined:
5 years, 1 month ago
Email:
a***********@libero.it

Posts by aristotele_m

<prev • 18 results • page 1 of 2 • next >
0
votes
1
answer
473
views
1
answers
Comment: C: deseq2 outliers problems
... Thanks now works. But I have only this series where I need that comand. What could be the reason? Is a bug or  don't change so much because I have always I very  low p-value (^-18)   ...
written 2.5 years ago by aristotele_m30
0
votes
1
answer
473
views
1
answers
Comment: C: deseq2 outliers problems
... Gruop  A  express GFP and Group B express my target genes. So I want to understand the effect of  overexpression of my gene on  my transcriptome. I know are overexpressed and also my count demonstate are overexpressed but the fold change are not close with my ratio calclulate from the counts. Is it ...
written 2.5 years ago by aristotele_m30
0
votes
1
answer
473
views
1
answer
deseq2 outliers problems
... Dear all, I have this situation for a gene overexppressed: Group A: average 85.33 GroupB: average 23081.19 average gene 1930.54 On the result table  of differential expression: basemean: 1930.54,log2Foldchange 5.115 lfcSE 0.341 The results seem more different from  the ratio obtained..  I fo ...
deseq2 written 2.5 years ago by aristotele_m30
0
votes
1
answer
1.0k
views
1
answer
Low count of differential expression data using Deseq2
... I have compare 2 group of  sample (4 vs 2 control).  I use standar ùDESEq2 pipeline but I have obtain this results: Pca show not homogeneous group . summary(res) out of 35000 with nonzero total read count adjusted p-value < 0.1 LFC > 0 (up) : 2, 0.0063% LFC < 0 (down) : 1, 0.0031% ...
deseq2 written 4.2 years ago by aristotele_m30 • updated 4.2 years ago by Michael Love26k
0
votes
2
answers
1.8k
views
2
answers
Use surrogate variables on DESeq2
... Hi! I have this problem. I want to model a surrogate variable on my data. I have two  two type of tumors but the PCA can not  show the separation between that. I try to use sva as describe in vignette  but I found this error:   dat <- counts(dds, normalized=TRUE) idx <- rowMeans(dat) > ...
deseq sva deseq2 differential gene expression written 4.3 years ago by aristotele_m30 • updated 3.4 years ago by szenitha0
0
votes
2
answers
799
views
2
answers
Comment: C: Deseq2 number of fragments use for differential expression
...   I use this code: colSums(counts(dds))/1e6   I use the Total starnde from illumina. How can verify by eye how appear on IGV? I mean how appear the reverse stranded  library? Thanks so much!!   ...
written 4.3 years ago by aristotele_m30
0
votes
2
answers
799
views
2
answers
Comment: C: Deseq2 number of fragments use for differential expression
... Thanks so much!!!I use this code: mkdir -p Count && mkdir -p tmp && ~/usr/local/bin/samtools sort -no ALIGN/120/Aligned.sortedByCoord.out.bam tmp/120 |samtools view - | htseq-count --mode=intersection-nonempty --stranded=reverse --type=exon --idattr=gene_id - Trasc_GH37_74/Homo ...
written 4.3 years ago by aristotele_m30
0
votes
2
answers
799
views
2
answers
Deseq2 number of fragments use for differential expression
... Dear All! I have align  a total stranded RNA using STAR and count the gene level using htseq count. All the sample on RNASeqQC have more then 60ML of total reads and more than 40 ML of uniq reads, When I import on DESeq2 object and I try to see the number of element I found this: colSums(assay( ...
deseq2 start written 4.3 years ago by aristotele_m30 • updated 4.3 years ago by Michael Love26k
0
votes
1
answer
835
views
1
answer
Deseq2 and gene clustering
... Hi! I use this tutorial  on this site http://www.bioconductor.org/help/workflows/rnaseqGene/: library("genefilter") topVarGenes <- head(order(-rowVars(assay(rld))),35) Why  -rowVars?       ...
clustering deseq2 written 4.7 years ago by aristotele_m30 • updated 4.7 years ago by Michael Love26k
0
votes
3
answers
6.0k
views
3
answers
Answer: A: Deseq2 supervised heatmap
... This is the results o differential expression.: out of 24250 with nonzero total read count adjusted p-value < 0.1 LFC > 0 (up) : 123, 0.51% LFC < 0 (down) : 163, 0.67% outliers [1] : 0, 0% low counts [2] : 1213, 5% (mean count < 3.1) [1] see 'cooksCutoff' argument of ?resul ...
written 4.7 years ago by aristotele_m30

Latest awards to aristotele_m

Great Question 2.5 years ago, created a question with more than 5,000 views. For deseq2 filter the low counts
Great Question 2.5 years ago, created a question with more than 5,000 views. For Deseq2 supervised heatmap
Epic Question 2.5 years ago, created a question with more than 10,000 views. For deseq2 filter the low counts
Popular Question 2.5 years ago, created a question with more than 1,000 views. For How to use SamR
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Use surrogate variables on DESeq2
Popular Question 4.2 years ago, created a question with more than 1,000 views. For deseq2 filter the low counts
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Deseq2 supervised heatmap

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 417 users visited in the last hour