User: szenitha

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szenitha0
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Posts by szenitha

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Comment: C: DESeq2 ANOVADEV giving strange result
... Apologies. I went over my code again and realized why I was getting such an output. There was a problem during reading of a file.My code works fine now. Thank you for helping me out.   ...
written 2.0 years ago by szenitha0
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Comment: C: DESeq2 ANOVADEV giving strange result
... Thank you Michael. I now included the surrogate variables and I'm still getting the same output. dds<-DESeq(ddssva,test = "LRT",reduced = ~SV1+SV2+SV3) ...
written 2.0 years ago by szenitha0
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DESeq2 ANOVADEV giving strange result
... Hello All, I am using DESeq2 to perform something like a one-way ANOVA. When I tried running the code on the datasets I have, it seems to be working fine for all except for one dataset. This dataset is from the organism fly while the others are either mouse or human.When I  run deseq2 with 'LRT' fo ...
deseq2 anova written 2.0 years ago by szenitha0 • updated 2.0 years ago by Michael Love20k
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Regarding batch effect in Deseq2 package
... Hello All, I have a some questions regarding batch effects.  In the workflow ,the sva package is used to find the source of unwanted variation and used the function stripchart to see how well the SVA method did at recovering these variables. Could you please explain the result returned by the metho ...
sva deseq2 svaseq written 2.2 years ago by szenitha0 • updated 2.2 years ago by Michael Love20k
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Comment: C: can we use sva function to estimate artifacts for rna seq data?
... Thank you jeff. Yes I now transformed the data using deseq2 and then used sva. Now I am getting the same result as earlier. Just to confirm . sva needs transformed data like log2 or rlog or voom tranformation as input. svaseq takes count data and then log transforms it. So the difference would be in ...
written 2.3 years ago by szenitha0
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can we use sva function to estimate artifacts for rna seq data?
... Hello all, I have a question regarding the sva function. To start with I am analysing a RNA seq dataset. My condition consists of 4 groups(CON_GM,CON_WM,MS_GM and MS_WM). CON is the control and MS is patients affected with multiple sclerosis. GM(grey matter) and WM(white matter) are cell types. I f ...
sva batcheffectcorrection svaseq written 2.3 years ago by szenitha0 • updated 2.3 years ago by Jeff Leek520
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Comment: C: Large foldchange values while analyzing rna seq data using limma
... ok. Thank you. ...
written 2.3 years ago by szenitha0
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Comment: C: Large foldchange values while analyzing rna seq data using limma
... I am actually normalizing the data using deseq2 and then filtering out genes which do not have a max expression of 10 in atleast one of the conditions. should I be normalizing the data only using limma? ...
written 2.3 years ago by szenitha0
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Large foldchange values while analyzing rna seq data using limma
... Hello everyone, I am new to data analysis and having trouble while trying to analyze rna-seq data using limma package. My RNA-seq data has 3 conditions(ifected lung,infected spleen,non infected spleen) and I am doing 2 things. Firstly I perform anova and then I define contrast and try to get the di ...
limma logfoldchange written 2.3 years ago by szenitha0 • updated 2.3 years ago by Aaron Lun21k
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Comment: C: DESeq2: Extremely low pvalues
... Yes. I understand now. Thank you for helping me out.  ...
written 2.3 years ago by szenitha0

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