User: exin

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exin50
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Posts by exin

<prev • 22 results • page 1 of 3 • next >
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Comment: C: When exactly is a gene "expressed"?
... Thank you Charles! ...
written 1 day ago by exin50
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Comment: C: When exactly is a gene "expressed"?
... Probably stats/ bioinformatics. Especially the part on dealing with genes with exceptionally large transcript counts across all samples. ...
written 1 day ago by exin50
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Comment: C: When exactly is a gene "expressed"?
... Thank you for such a practical answer! ...
written 1 day ago by exin50
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When exactly is a gene "expressed"?
... I'm interested in comparing the genes that are expressed in several cell types in order to infer functionings of these cell types. I use DESeq to find genes that are differentially expressed (DE). However, a gene doesn't always have to be DE to be involved in the functionings of a cell. So ideally ...
gene expression rna-seq written 2 days ago by exin50 • updated 2 days ago by Charles Warden6.5k
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Comment: C: DESeq: obtaining DEGs from uneven dataset (some with replicates, some without)
... Thanks ATpoint. Besides treating it as an exploratory analysis / not drawing firm conclusions from the dataset, I'm wondering how exactly to augment the test / result, by accepting the assumption that variance-mean estimates from replicated samples can be applied to unreplicated ones? ...
written 12 days ago by exin50
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DESeq: obtaining DEGs from uneven dataset (some with replicates, some without)
... I'm trying to perform differential gene expression analyses using DESeq, on a pre-existing dataset, where 8 cell types (A to H) were identified from MARS-Seq on whole organism. Gene expression counts are given for A x 9 replicates B x 1 C x 1 D x 3 E x 1 F x 1 G x 4 H x 1 In order to find genes ...
gene expression rna-seq written 12 days ago by exin50
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Comment: C: sva combat removes wanted biological variation
... Ok I'll do that. Thank you Kevin!! ...
written 7 weeks ago by exin50
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sva combat removes wanted biological variation
... My sc-RNAseq on sponge larvae cells was done as 2 batches (library prepped separately, separate sequencing runs). Samples consist of 7 cell types, 8 replicates each: 5 reps in batch 1 and 3 reps in batch 2; except for one cell type, which went to batch 2. I use combat in the sva package to remove ...
R sva combat rna-seq pca written 7 weeks ago by exin50 • updated 7 weeks ago by zx87546.8k
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Comment: C: What is ERCC spike-in really saying about my sequencing run?
... Thank you for your insights Kevin! ...
written 6 months ago by exin50
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What is ERCC spike-in really saying about my sequencing run?
... I've used ERCC spike-in to prep the library for my recent run of sc-RNA seq. Looking at the plot of ERCC read counts vs ERCC concentration, I know we should ideally expect to see a nice correlation with R2 =1, for every sample in the library. Looking at the sequences itself, QC and mapping %, I'v ...
ercc spike-in rna-seq written 6 months ago by exin50

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