User: Mozart
Mozart • 190
- Reputation:
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Posts by Mozart
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... Hello everyone,
I am working on a case study where distribution of p values, unfortunately, conservative rather than being anti-conservative. It's good to face difficulties as they *forge your patience* but I guess this is where it comes the hard bit.
Based on [this post][1] and [this other post][ ...
written 7 hours ago by
Mozart • 190
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... Thanks for the useful hints ATpoint and yeah, I totally agree about the usefulness of this platform! In the light of this, one more question if you don't mind. I noticed that once the matrix is corrected by using the `cleaningP` function:
cleaningP = function(y, mod, svaobj, P=ncol(mod)) {
...
written 1 day ago by
Mozart • 190
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... Thanks ATpoint,
that basically solved my problem. It really sounds so reassuring how important this forum could be in the learning process. It's good to have a good string of code to use for all the pipelines, to be honest.
Thanks a million.
...
written 1 day ago by
Mozart • 190
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... Hello everyone,
I am trying to understand how to show a PCA plot on SVA-corrected counts by using DESeq2 (I know that expert guys tend to prefer some other tools but I need this for a presentation). Many posts out there (like [this][1], [this][2] and [this][3]) but none of them seem to address exact ...
written 2 days ago by
Mozart • 190
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Comment:
C: Heatmap with just two columns
... Thanks a lot!! I will do! ...
written 12 days ago by
Mozart • 190
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Comment:
C: Heatmap with just two columns
... Thanks so much for your reply. Sometimes it is hard to change someone else's mind, if you know what I mean!
It's all about being persuasive and kind at the same time but it's just hard sometimes.
But thanks a lot, I do appreciate the fact that the common way of doing this is actually the usual appro ...
written 12 days ago by
Mozart • 190
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... Hello everyone,
I have been asked to summarise information from my count matrix - obtained from 4 replicates - in just two columns (one column per group).
What's the best approach to do this?
I usually use the following steps to get a classical heatmap containing as many tiles as per replicate
...
written 12 days ago by
Mozart • 190
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... Thanks a lot for this clarification. I will try to look at the Omicsoft deeper if I can. But what if one has to draw conclusions for like 'defending' the idea according to which both tools are used (I mean, IPA and GSEA)?
...
written 23 days ago by
Mozart • 190
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... Dear all,
I have read a couple of papers where people used both GSEA and IPA for their analysis in their pipeline and tried to justify this approach by saying that they tried to confirm results found in IPA with GSEA too. What do you think? Does it make any sense to you?
regards, ...
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... Thanks a lot Kevin for these useful information. I think it would be really important to be in touch with the sequencing facility in order to understand what is going on with my samples.
fingers crossed! ...
written 26 days ago by
Mozart • 190
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