User: sherajilir

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sherajilir0
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Posts by sherajilir

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Microarray Data Analysis CDF Problem
... Thanks a lot Guido, it worked finally! ...
written 3 months ago by sherajilir0
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Microarray Data Analysis CDF Problem
... Hello Everyone, I am trying to normalize a dataset GSE45220 based on hugene.1.1.st.v1 platform. However, when i try to do rma or gcrma normalization, i get an error about the missing cdf-file which does not work for the package anyway. #GSE45220 BiocManager::install("GEOquery") librar ...
microarray normalization written 3 months ago by sherajilir0 • updated 3 months ago by Guido Hooiveld2.5k
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Answer: A: Downloading HTSeq raw reads with TCGABiolinks
... Ok problem solved! Seems like the package has trouble of compatibility with R3.5.3. Updated to R3.6.0 and reinstalled the package. ...
written 3 months ago by sherajilir0
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Downloading HTSeq raw reads with TCGABiolinks
... Hello Everyone! I have been trying for a while to download BRCA RNASeq data using TCGAbiolinks package from bioconductor. I followed the protocol online and everything works perfectly till GDCprepare step, where i get an error. My code is as follows: #BRCA HT-Seq extraction with TCGAbiolinks ...
rnaseq tcgabiolinks written 4 months ago by sherajilir0
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Comment: C: Deseq2 PCA Anlysis
... Thanks Michael, I cannot do that since i cannot process the raw files due to lack of computational power. I am relying on raw counts from TCGA extracted by TCGABiolinks. ...
written 7 months ago by sherajilir0
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Deseq2 PCA Anlysis
... Hello everyone. I am doing differential expression analysis for a TCGA data set. When i checked PCA separation, i got something like this, a matter i have seen in GSEA as well. Two tumor samples are not separated from the normal. https://drive.google.com/file/d/1UZh-FQdCw9biCv9AzlfCLAzxLV008cSi/ ...
deseq2 pca written 7 months ago by sherajilir0 • updated 7 months ago by Michael Love25k
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Comment: C: DESEQ2 Batch effect
... Sorry for writting separately but just came to my mind to use shrinkage with apeglm package and got this https://drive.google.com/file/d/1ygZ1n9J_3he0L5ecFRFRTIPJV6TRzmmE/view?usp=sharing Now i think the problem is solved, though your feedback would be highly valuable. Thanks again ...
written 7 months ago by sherajilir0
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Comment: C: DESEQ2 Batch effect
... Thank you Michael for your prompt response. I did normalization and i'm getting an MA plot like this https://drive.google.com/file/d/1QeCzKQcTR5A-Wx7kGU52MvhfEj-27eCH/view?usp=sharing Do you think its acceptable? I have doubts because its not aligned to zero. Thank you once again ...
written 7 months ago by sherajilir0
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Comment: C: Annotating protein sequences
... I did not quite understand! You have protein sequences in your hand and want to classify them according to domains? ...
written 7 months ago by sherajilir0
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DESEQ2 Batch effect
... Hello everyone, I am analyzing coad-tcga dataset and there are two sequencing platforms used, illuminaHiseq and IlluminaGA. Is there a way to remove batch effects in DESeq2 package prior to differential expression or does the GLM remove it automatically (which i dont hink happens). Thanks! ...
deseq2 batch written 7 months ago by sherajilir0 • updated 7 months ago by Michael Love25k

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