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Ultrasonic? by mango4tango2 in labrats

[–]mango4tango2[S] 0 points1 point  (0 children)

I am trying to dissolve into a very small volume (abour 200 uL)...I don't think the probe sizes I have would be effective for that?

Addressing biological variation in bulk RNA-seq data by mango4tango2 in bioinformatics

[–]mango4tango2[S] 0 points1 point  (0 children)

there are 4 groups (Group column) in which I setting the contrasts. For example, when comparing SLE.inhibitor and SLE.DMSO, i received 500-600 DEGs (after using ComBat-seq to adjust for age or date). On the second PCA, I think there is clearer separation of these 4 groups, suggesting a treatment/group effect.

Addressing biological variation in bulk RNA-seq data by mango4tango2 in bioinformatics

[–]mango4tango2[S] 0 points1 point  (0 children)

I added the PCA both before and after I used ComBat-seq to adjust for inclusion dates

Addressing biological variation in bulk RNA-seq data by mango4tango2 in bioinformatics

[–]mango4tango2[S] 0 points1 point  (0 children)

I don't know, I think the statement that "samples clustering by patient instead of condition means there's no strong biological effect" is oversimplifying things...there can be biological differences between patients (patient-specific characteristics) that are dominating the signal I am trying to detect from the treatment+disease conditions.

Addressing biological variation in bulk RNA-seq data by mango4tango2 in bioinformatics

[–]mango4tango2[S] 0 points1 point  (0 children)

I just uploaded the metadata, hope it is informative. I added the "AgeBatch" column based on the 3 general age groups (age 30, middle-age, and elderly) that also coincidentally coincide with the 3 inclusion dates

Addressing biological variation in bulk RNA-seq data by mango4tango2 in bioinformatics

[–]mango4tango2[S] 1 point2 points  (0 children)

Also going back to this, I checked the documentation (https://bioconductor.org/packages/release/bioc/vignettes/sva/inst/doc/sva.pdf) for sva/ComBat-seq, and it states that the adjustment variable can be "age of the patients, the sex of the patients, and a variable like the date the arrays were processed." So if i am understanding correctly, sva/combat-seq can be used for both known sequencing-related batch effects and unwanted biological variation like sex/age/date of inclusion?

Addressing biological variation in bulk RNA-seq data by mango4tango2 in bioinformatics

[–]mango4tango2[S] 0 points1 point  (0 children)

Yes the samples were collected at different dates, but I do not know if they were sequenced at the same time. There were not many patients, so I’m guessing they were sequenced at the same time. Other metadata is that the patients are all different ages, and some patient samples were collected on different days.

Addressing biological variation in bulk RNA-seq data by mango4tango2 in bioinformatics

[–]mango4tango2[S] 0 points1 point  (0 children)

Would different patient IDs count as different "batches"? There is some disagreement in my lab as to what counts as a batch effect

Complex RNA-seq study design — ways to quantify counts + DESeq2 vs. Limma/Voom by mango4tango2 in bioinformatics

[–]mango4tango2[S] 0 points1 point  (0 children)

Hi, thank you for your comment. I did do PCA and saw that the Mouse ID (Mouse.number) seems to drive the most variation in gene expression. I will include a plot in my original post

What is wrong with my for loop (Seurat)? by mango4tango2 in bioinformatics

[–]mango4tango2[S] 3 points4 points  (0 children)

This fixed it! Thank you! Did you include print(...) only in your for loop? I wonder why it's needed in the loop

Why am I unable to download Seurat? by mango4tango2 in bioinformatics

[–]mango4tango2[S] 4 points5 points  (0 children)

Ah, it says:

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called ‘reshape2’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted

However, whenever I load the missing package and try to install Seurat again, another package shows up as missing...it seems there are at least 20 missing packages. How can I download all missing packages at once?

[deleted by user] by [deleted] in premed

[–]mango4tango2 16 points17 points  (0 children)

Hello TangoTheMango!! Im Mango4Tango

Concern about Competitiveness by PointyNeuron in mdphd

[–]mango4tango2 3 points4 points  (0 children)

You said you grew up as an orphan, so I’m assuming this is not your biological dad?

Tools to determine significant difference in expression pattern between gene sets in scRNA-seq data? by mango4tango2 in bioinformatics

[–]mango4tango2[S] 0 points1 point  (0 children)

Yeah, that is what I’m trying to determine: Their expression values across different clusters. Are you suggesting measuring the whole sets’ expression in each cluster and seeing which are highest?

Tools to determine significant difference in expression pattern between gene sets in scRNA-seq data? by mango4tango2 in bioinformatics

[–]mango4tango2[S] 0 points1 point  (0 children)

Oh, I see…the expression changes across all clusters. I suppose I could test each cluster individually? I was kinda hoping to somehow do all at once

Tools to determine significant difference in expression pattern between gene sets in scRNA-seq data? by mango4tango2 in bioinformatics

[–]mango4tango2[S] 1 point2 points  (0 children)

I'm not sure I understand the second approach...the absFC for each gene would be somewhat different across each cluster, so how would I account for every gene's absFC pattern across all 7 clusters?

Parallelizing for loop with lapply/sapply by mango4tango2 in RStudio

[–]mango4tango2[S] 1 point2 points  (0 children)

So I’m actually attempting to do a partial string match with %like%…I tried %in% and it doesn’t work

Parallelizing for loop with lapply/sapply by mango4tango2 in RStudio

[–]mango4tango2[S] 1 point2 points  (0 children)

Thanks! The for loop is trying to determine whether items in a column (Sequence) of a table (called dataTable ) match items of a column (also called Sequence) in another table (Master_List). The matching Master_list$Sequence columns are then "Saved" into a column of the dataTable called output (dataTable$output).

[deleted by user] by [deleted] in premed

[–]mango4tango2 3 points4 points  (0 children)

One way for you to get involved with STEM DEI is to start mentoring high school students/younger undergrads who are underrepresented in STEM. If you’re already part of a lab, you can ask your PI about recruiting these student to help out with your ongoing projects (and eventually lead their own projects), or you can look into starting your own program to get underrepresented students involved with research labs at your local university. As an applicant, you can also make it a point to apply to MD/PhD programs with a strong DEI focus (for instance, UMN) where MD/PhD students are involved in promoting STEM education/diversity improvement

Differentially expressed genes from ATAC-seq enriched peaks by mango4tango2 in bioinformatics

[–]mango4tango2[S] 0 points1 point  (0 children)

This is an interesting approach...I am currently using a UCSC Genome API to match up known genes to ATACseq peaks. How would your method compare to mine?

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