User: Lin

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Lin40
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Posts by Lin

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Comment: C: RNA-seq normalization without filtering
... Thanks for your answer! Indeed, this was more a general question (but of course the code is also helpful because I need to do it with my data). As Mikhael mentioned I also read in the edgeR workflow that filtering comes before normalization. And now I was wondering if there is a pipeline where it wo ...
written 13 days ago by Lin40
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RNA-seq normalization without filtering
... Hi all, I have a basic question regarding the normalization of RNAseq data - I understand why we have to normalize the raw counts, but I do not fully understand the biological details and I am confused about the differences between methods - so sorry if the answer is obvious. Basically, I have ~ * ...
rnaseq normalization edger deseq2 written 15 days ago by Lin40 • updated 15 days ago by Steve Lianoglou12k
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use differences in expression as input for co-expression network?
... Hi all, if I have expression data from two time-points and I am interested in changes over time- Would it be possible to use the difference in expression between the time-points (delta values) as input for WGCNA (or for co-expression networks in general)? I am not sure if there could be a problem ...
wgcna co-expression written 5 weeks ago by Lin40 • updated 21 days ago by mikhael.manurung160
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Comment: C: RNA-Seq normalization for co-expression analysis
... Yes, exactly, that would be what I thought of... Because I need normalized data, but would like to use another filtering procedure during the co-expression analysis... And with this filter I would loose too many transcripts before (and would double-filter). ...
written 5 weeks ago by Lin40
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Comment: C: RNA-Seq normalization for co-expression analysis
... Hi Kevin, thanks for your answer! But my question was rather if there is a problem using TMM normalization FIRST (with unfiltered data), and filter the data afterwards (because I want to use another pipeline where the whole filtering is implemented). ...
written 6 weeks ago by Lin40
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RNA-Seq normalization for co-expression analysis
... Hi all, it is my first time to work with RNA-seq data, and with this data a differential expression analysis and co-expression network analysis should be done. Now I read in the pipeline [RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR] for differential expression analysis that *at f ...
limma edger wgcna written 6 weeks ago by Lin40 • updated 5 weeks ago by Gordon Smyth38k
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Comment: C: WGCNA: relate modules to binary trait
... I used the CEMiTool function for filtering! I was just thinking that the end result with ~ 5000 genes is good, so I did not change the filter value. What do you think about the plot of mean and variance, it does not look like I need the apply_vst parameter? And would you rather use pearson or spear ...
written 7 months ago by Lin40
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Comment: C: WGCNA: relate modules to binary trait
... Thanks for your answer Pedro! Do you think I should use a more stringent parameter, because I thought that ~ 5000 genes would be a good sample? I will attach a plot from the mean& variance [here][1]. I think the data shows no straight line, but what could I read further from this/ what would yo ...
written 7 months ago by Lin40
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Comment: C: WGCNA: relate modules to binary trait
... Thank you for your answer! The DE analysis was already done. There were some differences in for example immune-system related pathways, what makes sense regarding this disease. The most differences were observed for the 3. timepoint, what was the reason why I started to use this here. I wanted t ...
written 7 months ago by Lin40
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WGCNA: relate modules to binary trait
... Hey! I am going through the very helpful WGCNA tutorials and constructed a co-expression network, but now I am stuck with further steps and interpretation of my modules. At first some information regarding my data and progress:  I have 60 samples from humans (assigned to 2 groups a 30 people) ...
wgcna R module eigengene binary trait written 7 months ago by Lin40 • updated 7 months ago by pedrostrusso30

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