User: Jane Merlevede

Reputation:
90
Status:
Trusted
Location:
Last seen:
2 weeks, 6 days ago
Joined:
5 years, 8 months ago
Email:
j*************@gmail.com

Posts by Jane Merlevede

<prev • 74 results • page 1 of 8 • next >
0
votes
2
answers
232
views
2
answers
Comment: C: DESeq2 - PCAplot differs between rlog and vsd transformation
... Ok, thank you ...
written 22 days ago by Jane Merlevede90
0
votes
2
answers
232
views
2
answers
Answer: A: DESeq2 - PCAplot differs between rlog and vsd transformation
... Thank you for your response Michael. These 2 samples have not the lowest sizeFactor and there is no outlier among sizeFactors: summary(sizeFactors(dds)) Min. 1st Qu. Median Mean 3rd Qu. Max. 0.5952 0.8673 1.0220 1.0290 1.1430 1.5610 I'd go with vst because it is faster but I don ...
written 23 days ago by Jane Merlevede90
2
votes
2
answers
232
views
2
answers
DESeq2 - PCAplot differs between rlog and vsd transformation
... Dear all,   I am using DESeq2 on 63 RNASeq samples. The design used to explain the counts is based on the mutational status of 2 genes: ~GroupGene1+GroupGene2 I performed 3 PCA on this dataset: 1) on all the genes with rowSums(counts(dds)) > 10, that are in my case 36276 genes. The PCA are ...
deseq2 rlog transformation vsd plotpca written 23 days ago by Jane Merlevede90
0
votes
1
answers
147
views
1
answers
Comment: C: DESeq2 minReplicatesForReplace with different group size
... Okay. Thank you a lot for your help   ...
written 11 weeks ago by Jane Merlevede90
0
votes
1
answers
147
views
1
answers
Comment: C: DESeq2 minReplicatesForReplace with different group size
... Thank you Michael. If there were no extreme outlier, would you continue with minReplicatesForReplace=7 and cooksCutoff=FALSE or minReplicatesForReplace=4? That's just for curiosity because there are "extreme outliers". For example, there are 3 samples around 0 and 1 at 100 or 3 samples around 50 a ...
written 11 weeks ago by Jane Merlevede90
0
votes
1
answers
147
views
1
answers
Comment: A: DESeq2 minReplicatesForReplace with different group size
... Thank you Michael for your answer. When I use minReplicatesForReplace=Inf, there are 1295 outliers, while there are 472 with minReplicatesForReplace=7. With minReplicatesForReplace=7 (or minReplicatesForReplace=14), if I am right, outliers among the 14 tumor samples will be replaced by the mean of ...
written 12 weeks ago by Jane Merlevede90
2
votes
1
answer
147
views
1
answer
DESeq2 minReplicatesForReplace with different group size
... Dear DESeq2 users, I have an RNASeq experiment with 18 samples, 4 normal and 14 tumor. I am comparing the 2 conditions: normal vs tumor. I ran DESeq(dds,  minReplicatesForReplace=7) in order to remove outliers. By doing so, I remove outliers only from the tumor group from what I understand. I get: ...
deseq2 written 12 weeks ago by Jane Merlevede90
0
votes
1
answer
204
views
1
answer
tri.counts.method parameter in deconstructSigs
... Dear deconstructSigs users, I am using deconstructSigs on WES data from hypermutated tumors: whichSignatures = whichSignatures(tumor.ref = sigs.input, signatures.ref = signatures.cosmic, sample.id = "MyPatient", associated = c(),signatures.limit = NA, signature.cutoff = 0, contexts.needed = TRUE, ...
deconstructsigs written 6 months ago by Jane Merlevede90 • updated 6 months ago by boostoo0
0
votes
0
answers
143
views
0
answers
ConsensusClusterPlus - Intrepretation of item & cluster consensus plots
... Hello,   I do not understand why the scale in item-consensus plot goes from 0 to 1.4. Since I used pItem=0.8, I thought the values would go from 0.8 to 1.2. I assumed this plot indicates for a particular sample its frequency of assignment to each cluster. In cluster-consensus plot, the scale goes ...
consensusclusterplus written 7 months ago by Jane Merlevede90
0
votes
0
answers
177
views
0
answers
ConsensusClusterPlus - add labels to plot
... Dear ConsensusClusterPlus users,   Is it possible to add labels (colnames of the data matrix) on the plots generated by ConsensusClusterPlus: dendograms of consensus matrix, tracking plots and item consensus barplots? It would be nice to see the cluster membership of each sample across the number ...
consensusclusterplus written 7 months ago by Jane Merlevede90

Latest awards to Jane Merlevede

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 229 users visited in the last hour