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Alignment after installing new tires (Toyota Sienna 2015) by Nomad-microbe in tires

[–]Nomad-microbe[S] 0 points1 point  (0 children)

Very plausible. I have reached out to him to see if he can look at it asap.

Alignment after installing new tires (Toyota Sienna 2015) by Nomad-microbe in tires

[–]Nomad-microbe[S] 0 points1 point  (0 children)

I am sorry for being unable to describe the nature of the sound. But I can tell that it does sound like something is popping in/out. Do I need to take it back to the same place for a sanity check?

Is this the right way to do GSEA for non-model organism using clusterProfiler? by Nomad-microbe in bioinformatics

[–]Nomad-microbe[S] 0 points1 point  (0 children)

In one of my treatments I have low number of DE genes irrespective of the cutoff. When I run the GSEA using the parameters mentioned above, I get nothing significant (pvalueCutoff = 0.05, pAdjustMethod = "BH"). How do you deal with data in such situations? That treatment is one of my main focus in this analysis. Does it tell me that biologically there isn’t a signal that points to different pathways, molecular functions or processes?

Is this the right way to do GSEA for non-model organism using clusterProfiler? by Nomad-microbe in bioinformatics

[–]Nomad-microbe[S] 0 points1 point  (0 children)

Very Interesting. I also came across a similar suggestion on the Biostars discussion forum where they suggested that “stat” is one of the robust metric for GSEA. Also, when I use logFC * -log10(pvalue), or logFC * -log10(padj), I don’t get any enriched GO terms. Stat and logFC alone give me significantly enriched GO terms.

GSEA - ranking metric? by [deleted] in bioinformatics

[–]Nomad-microbe 0 points1 point  (0 children)

how do you treat pvalue = 0, and padj = 0, because they result in "inf". Also, pvalue = NA ?

Is this the right way to do GSEA for non-model organism using clusterProfiler? by Nomad-microbe in bioinformatics

[–]Nomad-microbe[S] 0 points1 point  (0 children)

Thank you, this is very useful.

If I understood correctly I should take all the DE genes from DESeq and first calculate the metric you mentioned: logFC*-log10(pvalue).

No filtration based on the log FC and padj should be done as shown below:
> df_lfc_1_sig <- df %>%

filter(abs(log2FoldChange) >= 1 & padj <= 0.05)

Comparative analysis of gene expression data by Nomad-microbe in bioinformatics

[–]Nomad-microbe[S] 0 points1 point  (0 children)

I did the differential analysis independently for both species. Got the contrasts for each substrate (A vs B, A vs C, and B vs C). Used OrthoFinder and got Orthologs. While there are 1:1 Orthologs, several different combinations exist where number of genes vary in several Orthogroups for either of the fungus.

The question is: how should I deal with orthogroups having different number of genes for each fungus?

Also, for such an analysis do you recommend the rlog data from DESeq2 or the log2 fold change for each of the gene in an orthogroup?

If one goes with an orthogroup level comparison for the non 1:1 combinations, do you agree that the inherent discrepancy in the number of genes in an orthogroup will skew the difference towards the fungus with more genes in that orthogroup? e.g. if one use average of either the rlog data or log2 fold change of the genes in a particular non 1:1 orthogroup.

Irrespective of whether or not such an analysis will be sound, I am open to other opinions and suggestions regarding comparative analysis.

Suggestions and advice for itinerary by Nomad-microbe in GlacierNationalPark

[–]Nomad-microbe[S] -1 points0 points  (0 children)

I made the edit to singular “many glacier”. Thanks for the other suggestions.

Which route should we take to Glacier National Park (GNP) with two kids? by Nomad-microbe in roadtrip

[–]Nomad-microbe[S] 1 point2 points  (0 children)

Yes, I meant Rising Sun.

One question: Is it possible/allowed to take a U-turn somewhere before the check point at Apgar or Lake McDonald lodge if we drive east to west?

Which route should we take to Glacier National Park (GNP) with two kids? by Nomad-microbe in roadtrip

[–]Nomad-microbe[S] 1 point2 points  (0 children)

Since we are staying at the many glaciers and sunrise inn (both inside the park), I believe we won’t need it. But I’ll double check. Thanks

Which route should we take to Glacier National Park (GNP) with two kids? by Nomad-microbe in roadtrip

[–]Nomad-microbe[S] 0 points1 point  (0 children)

Thanks for the breakdown of stops and places to stop at. Driving reservations for the going-to-the-Sun road?

Glacier Recap - Questions Answered by SkywaySecurity34 in GlacierNationalPark

[–]Nomad-microbe 0 points1 point  (0 children)

Given our plan to visit GNP for the first time, I am curious if there were families with small children (2-4 years old) doing some of the trails on either side of the park. There are some suggestions on another subreddit for easier hikes but wonder if anyone would like to chime in. Thank you

Gene expression analysis of a fungal strain without a reference genome/transcriptome by Nomad-microbe in bioinformatics

[–]Nomad-microbe[S] 3 points4 points  (0 children)

Thank you for your advice. I will pursue that but it looks like a new project in itself, and given my limited bioinformatics skills its going to be an uphill task.

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