User: lirongrossmann

Reputation:
0
Status:
New User
Location:
Last seen:
3 days, 15 hours ago
Joined:
2 months, 1 week ago
Email:
l*************@yahoo.com

Posts by lirongrossmann

<prev • 37 results • page 1 of 4 • next >
0
votes
1
answer
67
views
1
answer
Distribution of transformed data using VST
... Hi Everybody, I would like to use variance stabilizing transformation on rna seq raw count samples to build a machine learning model in order to predict two classes. I wanted to use linear discriminant analysis, but was not sure if I can assume that the transformed data are distributed normally.  ...
deseq2 variancestabilizingtransformation written 7 days ago by lirongrossmann0 • updated 7 days ago by Michael Love14k
0
votes
1
answer
77
views
1
answer
Deseq2 for small matched samples
... Hi everyone, I have 16 rna seq samples (not replicates) and I want to compare 8 vs 8 which are paired matched. Are there any adjustments when using Deseq I can make for the small sample size and pairwise comparisons? Thanks! ...
deseq2 written 13 days ago by lirongrossmann0 • updated 13 days ago by Michael Love14k
0
votes
1
answers
94
views
1
answers
Comment: C: calculating logfold change from variance stabilizing transformation
... Thank you so much!  I see that SamSeq requires normalized data to run. From your experience, is it “safe” to give SamSeq the output of variance stabilizing transformation from Deseq2 as the input for the analysis. ...
written 20 days ago by lirongrossmann0
0
votes
1
answers
94
views
1
answers
Comment: C: calculating logfold change from variance stabilizing transformation
... My groups are small (9 vs 9 samples) and for some reason when I tried a different statistical test to compare them (Wilcoxon rank sum test, to be specific), I got a more uniform expression within each group for the genes that were significant. When I used Deseq to perform the statistical test, the g ...
written 20 days ago by lirongrossmann0
2
votes
1
answer
94
views
1
answer
calculating logfold change from variance stabilizing transformation
... Hi All, I am interested in calculating the logfold change from the transformed expression file obtained by using variance stabilizing transformation function.  I used the transformed data to normalize my count data and compare two groups within the data using a different statistical test than the ...
deseq2 variancestabilizingtransformation logfoldchange written 20 days ago by lirongrossmann0 • updated 20 days ago by Michael Love14k
0
votes
1
answers
111
views
1
answers
Comment: C: comparing strand-specific counts to unstranded counts
... thank you!  My goal is to choose the genes that best discriminate my two groups in terms of their response to the treatment and use them for downstream analysis.  Since I have a batch effect confounding the biological effect (response to treatment) I am not sure which genes to choose based on the ...
written 23 days ago by lirongrossmann0
0
votes
1
answers
111
views
1
answers
Comment: C: comparing strand-specific counts to unstranded counts
... Thank you. I think that what confuses me is how to interpret the overall result of which gene can be a good candidate to discriminate between the two groups I have from a biologic standpoint.  To be more specific - I have two groups, each has 10 samples. One group responded to therapy the other di ...
written 23 days ago by lirongrossmann0
0
votes
1
answers
111
views
1
answers
Comment: C: comparing strand-specific counts to unstranded counts
...  Thanks!  So basically it accounts for the batch in a linear fashion if it uses GLM.   ...
written 24 days ago by lirongrossmann0
0
votes
1
answers
111
views
1
answers
Comment: A: comparing strand-specific counts to unstranded counts
... Thanks! Does Deseq2 treat the batch effect as a linear covariate or does it take into account non linear variations that the batch may include? ( I.e other than an offset) ...
written 24 days ago by lirongrossmann0
0
votes
1
answers
85
views
1
answers
Comment: C: Quantile normalization and Deseq2
... Thanks, I just wanted to make sure that genes that have "low" counts in two samples are comparable (i.e. have similar rank for example). ...
written 24 days ago by lirongrossmann0

Latest awards to lirongrossmann

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: 280 users visited in the last hour